RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780620|ref|YP_003065033.1| iron-responsive
transcriptional regulator [Candidatus Liberibacter asiaticus str.
psy62]
(144 letters)
>3lwf_A LIN1550 protein, putative transcriptional regulator; structural
genomics, JOI for structural genomics, JCSG; HET: SO4;
2.06A {Listeria innocua}
Length = 159
Score = 125 bits (315), Expect = 4e-30
Identities = 35/136 (25%), Positives = 65/136 (47%), Gaps = 9/136 (6%)
Query: 1 MHLTKRTDYGIRVLMYCAIH-NDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59
M +T + YG+ + + A D P + IA+ +SE +L +++ PL AGIV+++RG
Sbjct: 20 MKITTKGRYGLTITLELAKRIGDGPISLRSIAQDKNLSEHYLEQLIGPLRNAGIVKSIRG 79
Query: 60 RRGGVRLCRPADQITILDVVKATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNAFF 119
GG L ++IT D+++ E + E + + + NA
Sbjct: 80 AHGGYVLNGDPEKITAGDIIRTLEGPIVLVESMEDEE--------AAQRELWTRMRNAVR 131
Query: 120 DVLTQYSIECLVRNRS 135
DVL Q ++ L+++ +
Sbjct: 132 DVLDQTTLSDLLKHST 147
>1ylf_A RRF2 family protein; structural genomics, transcription regulator,
PSI, protein structure initiative; 2.50A {Bacillus
cereus atcc 14579} SCOP: a.4.5.55
Length = 149
Score = 97.9 bits (243), Expect = 9e-22
Identities = 32/137 (23%), Positives = 54/137 (39%), Gaps = 5/137 (3%)
Query: 1 MHLTKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60
M ++ R + +L + +AE+ + + + KI+ L +AG V RG
Sbjct: 7 MKISSRFSIAVHILSILKNNPSSLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNRGP 66
Query: 61 RGGVRLCRPADQITILDVVKATE--ESFFVAECFASHKIDCPL--VGSCGLTSVLRKALN 116
G L +IT+LDV A E + DCP+ L +L +A +
Sbjct: 67 GGAGLLKDL-HEITLLDVYHAVNVVEEDKLFHIHEQPNPDCPIGANIQAVLEIILIQAQS 125
Query: 117 AFFDVLTQYSIECLVRN 133
A +VL ++ L
Sbjct: 126 AMEEVLRNITMGQLFET 142
>1xd7_A YWNA; structural genomics, protein structure initiative, winged
helix DNA binding, hypothetical protein, PSI; 2.30A
{Bacillus subtilis subsp} SCOP: a.4.5.55
Length = 145
Score = 97.4 bits (242), Expect = 1e-21
Identities = 22/135 (16%), Positives = 51/135 (37%), Gaps = 5/135 (3%)
Query: 1 MHLTKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60
+ R I +L ++ IA++ + + + +++ L KA I+ + G
Sbjct: 2 SLINSRLAVAIHILSLISMDE--KTSSEIIADSVNTNPVVVRRMISLLKKADILTSRAGV 59
Query: 61 RGGVRLCRPADQITILDVVKATEESFFVAECFASHKIDCPL--VGSCGLTSVLRKALNAF 118
G P I++L+V +A ++ + + CP+ L A
Sbjct: 60 PGASLKKDP-ADISLLEVYRAVQKQEELFAVHENPNPKCPVGKKIQNALDETFESVQRAM 118
Query: 119 FDVLTQYSIECLVRN 133
+ L S++ ++ +
Sbjct: 119 ENELASKSLKDVMNH 133
>3k69_A Putative transcription regulator; putative transcriptional
regulator, structural genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.95A
{Lactobacillus plantarum}
Length = 162
Score = 96.7 bits (240), Expect = 2e-21
Identities = 23/142 (16%), Positives = 50/142 (35%), Gaps = 9/142 (6%)
Query: 1 MHLTKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60
++ + ++Y H D ++A++ ++ + + IL L K G + G+
Sbjct: 5 SNMKLDFSVAVHSILYLDAHRDSKVASRELAQSLHLNPVMIRNILSVLHKHGYLTGTVGK 64
Query: 61 RGGVRLCRPADQITILDVVKATEESFFVAECFASH-------KIDCPLV--GSCGLTSVL 111
GG +L + + D+ T F + P+ S LT +
Sbjct: 65 NGGYQLDLALADMNLGDLYDLTIPPTISYARFITGPSKTDEQADQSPIAANISETLTDLF 124
Query: 112 RKALNAFFDVLTQYSIECLVRN 133
A + Q+++ L +
Sbjct: 125 TVADRQYRAYYHQFTMADLQAD 146
>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 = 43.0 bits (101), Expect = 3e-05
Identities = 21/124 (16%), Positives = 39/124 (31%), Gaps = 44/124 (35%)
Query: 35 CISELF-LFKILQPLVKAGIVETVRGRRGGV--RLCR-PADQITI----LDVVK------ 80
EL L++ LV +++ L R D + L++++
Sbjct: 169 YFEELRDLYQTYHVLVGD-LIKFS----AETLSELIRTTLDAEKVFTQGLNILEWLENPS 223
Query: 81 ATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNAFFDVLTQYSIECLVRN------R 134
T + ++ S I CPL+ G+ L Y + + R
Sbjct: 224 NTPDKDYLL----SIPISCPLI---GVIQ------------LAHYVVTAKLLGFTPGELR 264
Query: 135 SSIK 138
S +K
Sbjct: 265 SYLK 268
Score = 29.5 bits (66), Expect = 0.33
Identities = 18/94 (19%), Positives = 28/94 (29%), Gaps = 27/94 (28%)
Query: 69 PADQITILDVVKATEE---SF--FVAECFASHKIDCPLVGSCGL-TSVLRKALNAF---F 119
P + D E F +V+ ++ G VL L F +
Sbjct: 44 PTEGFAADDEPTTPAELVGKFLGYVS-----SLVE---PSKVGQFDQVLNLCLTEFENCY 95
Query: 120 ----DV------LTQYSIECLVRNRSSIKKIFNA 143
D+ L Q + LV+ + IK A
Sbjct: 96 LEGNDIHALAAKLLQENDTTLVKTKELIKNYITA 129
Score = 28.8 bits (64), Expect = 0.47
Identities = 19/128 (14%), Positives = 36/128 (28%), Gaps = 55/128 (42%)
Query: 11 IRVLMY--CAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVE-------TVRGRR 61
I VL + + YPN + + + IL+ ++ E ++
Sbjct: 300 ITVLFFIGVRCYEAYPN--TSLPPS----------ILEDSLENN--EGVPSPMLSISN-- 343
Query: 62 GGVRLCRPADQITILDVVKAT--EESFFVAECFASHKIDCPLVGS-------------CG 106
L + Q ++ + +++ LV G
Sbjct: 344 ----LTQEQVQ-DYVNKTNSHLPAGK----------QVEISLVNGAKNLVVSGPPQSLYG 388
Query: 107 LTSVLRKA 114
L LRKA
Sbjct: 389 LNLTLRKA 396
>3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2,
protein structure initiative; 2.20A {Thermoplasma
acidophilum dsm 1728} SCOP: a.4.5.28 b.43.5.2
Length = 230
Score = 31.9 bits (72), Expect = 0.057
Identities = 12/63 (19%), Positives = 26/63 (41%), Gaps = 1/63 (1%)
Query: 1 MHLTKRTDYGIRVLMYCAIHNDYPN-RISQIAEACCISELFLFKILQPLVKAGIVETVRG 59
+ + I+ + A ++ S++A+ IS+ +I+ L K G +
Sbjct: 3 LETDDQYYRAIKKIKEAAEASNRAYLTSSKLADMLGISQQSASRIIIDLEKNGYITRTVT 62
Query: 60 RRG 62
+RG
Sbjct: 63 KRG 65
>2v79_A DNA replication protein DNAD; primosome, DNA remodelling,
oligomerization domain, DNA-binding protein; HET: DNA;
2.00A {Bacillus subtilis}
Length = 135
Score = 31.5 bits (71), Expect = 0.068
Identities = 7/52 (13%), Positives = 14/52 (26%)
Query: 14 LMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVR 65
+ Y +Q+ E IS L+ ++ G +
Sbjct: 41 IKMHLEKGSYFPTPNQLQEGMSISVEECTNRLRMFIQKGFLFIEECEDQNGI 92
>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix
prnai nucleotide-binding domain; HET: MSE; 1.80A
{Sulfolobus solfataricus}
Length = 244
Score = 31.6 bits (71), Expect = 0.079
Identities = 13/56 (23%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRL 66
+++L ++ I+++A+ SE L + L K GI+ +G+ V L
Sbjct: 155 MKLLN--VLYETKGTGITELAKMLDKSEKTLINKIAELKKFGILT-QKGKDRKVEL 207
>1p4x_A Staphylococcal accessory regulator A homologue; winged-helix
protein, transcription; 2.20A {Staphylococcus aureus}
SCOP: a.4.5.28 a.4.5.28
Length = 250
Score = 30.3 bits (68), Expect = 0.16
Identities = 8/48 (16%), Positives = 13/48 (27%)
Query: 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR 58
+L N + + E + L L K G + R
Sbjct: 161 FTILAIITSQNKNIVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKER 208
Score = 29.1 bits (65), Expect = 0.34
Identities = 10/48 (20%), Positives = 18/48 (37%)
Query: 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR 58
+L Y + +I C + L + ++ LVK + VR
Sbjct: 37 FILLTYLFHQQENTLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVR 84
>3eco_A MEPR; mutlidrug efflux pump regulator winged helix-turn-helix
motif, DNA-binding, transcription, transcription
regulation; 2.40A {Staphylococcus aureus}
Length = 139
Score = 29.9 bits (67), Expect = 0.19
Identities = 8/47 (17%), Positives = 17/47 (36%)
Query: 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR 58
L Y H + IA+A + + +L+ L + ++
Sbjct: 35 HTLGYLYAHQQDGLTQNDIAKALQRTGPTVSNLLRNLERKKLIYRYV 81
>2qc0_A Uncharacterized protein; NP_719793.1, uncharacterized protein,
structural genomics, joint center for structural
genomics, JCSG; HET: MSE; 1.60A {Shewanella oneidensis}
PDB: 3eqx_A*
Length = 373
Score = 29.8 bits (66), Expect = 0.24
Identities = 8/36 (22%), Positives = 15/36 (41%)
Query: 26 RISQIAEACCISELFLFKILQPLVKAGIVETVRGRR 61
RI + E+ L+ L G++E V+ +
Sbjct: 313 RIQNLVESGLAKRQTASVYLKQLCDIGVLEEVQSGK 348
>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple
frequency, 3D NMR, induced FIT, alternative splicing,
developmental protein; NMR {Homo sapiens}
Length = 159
Score = 29.5 bits (66), Expect = 0.30
Identities = 11/62 (17%), Positives = 19/62 (30%)
Query: 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEE 84
R I+ +S + KIL + G + ++ P I D +
Sbjct: 42 VRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPKVVEKIGDYKRQNPT 101
Query: 85 SF 86
F
Sbjct: 102 MF 103
>1uly_A Hypothetical protein PH1932; helix-turn-helix, structural
genomics, DNA binding protein; 2.50A {Pyrococcus
horikoshii OT3} SCOP: a.4.5.58 PDB: 2cwe_A
Length = 192
Score = 29.3 bits (65), Expect = 0.31
Identities = 13/58 (22%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCR 68
R + + N ISQ++E + ++ ++ L +AG+VE R G + +
Sbjct: 21 TRRKILKLLRNK-EMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKRTEMKGNLVEK 77
>1ku9_A Hypothetical protein MJ223; putative transcription factor,
homodimeric winged-helix fold, structural genomics,
PSI; 2.80A {Methanocaldococcus jannaschii} SCOP:
a.4.5.36
Length = 152
Score = 29.3 bits (65), Expect = 0.33
Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 1/47 (2%)
Query: 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR 58
V + + P IS I E IS+ + L+ L + G V V
Sbjct: 30 AVYAILYLSDK-PLTISDIMEELKISKGNVSMSLKKLEELGFVRKVW 75
>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein,
structural genomics, PSI- 2, protein structure
initiative; 3.00A {Corynebacterium diphtheriae}
Length = 583
Score = 29.0 bits (64), Expect = 0.43
Identities = 9/35 (25%), Positives = 12/35 (34%)
Query: 28 SQIAEACCISELFLFKILQPLVKAGIVETVRGRRG 62
S + C +S + LV V V G R
Sbjct: 534 SDLMAMCGVSRGTAKACVDGLVDEERVVAVGGGRS 568
>1o5l_A Transcriptional regulator, CRP family; TM1171, structural genomics,
JCSG, PSI, protein structure initiative; 2.30A
{Thermotoga maritima} SCOP: b.82.3.2
Length = 213
Score = 28.6 bits (63), Expect = 0.54
Identities = 10/64 (15%), Positives = 20/64 (31%), Gaps = 12/64 (18%)
Query: 14 LMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQI 73
M P + +++ + L ++ Q L + G +E R I
Sbjct: 154 HMNEKRELTLPVTLEELSRLFGCARPALSRVFQELEREGYIEKHGRR------------I 201
Query: 74 TILD 77
+L
Sbjct: 202 KVLK 205
>2vn2_A DNAD, chromosome replication initiation protein; DNA replication,
primosome; 2.3A {Geobacillus kaustophilus HTA426}
Length = 128
Score = 28.4 bits (63), Expect = 0.59
Identities = 5/50 (10%), Positives = 18/50 (36%)
Query: 14 LMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGG 63
+ +++AE +S ++++ L++ G++
Sbjct: 41 MQSFFEEGVLFPTPAELAERMTVSAAECMEMVRRLLQKGMIAIEEHTDEQ 90
>1x19_A CRTF-related protein; methyltransferase, bacteriochllochlorophyll,
BCHU, SAM, SAH, S-adenosylmethyonine,
S-adenosylhomocysteine, ADO-Met; 2.27A {Chlorobium
tepidum tls} PDB: 1x1a_A* 1x1b_A* 1x1c_A* 1x1d_A*
Length = 359
Score = 28.0 bits (61), Expect = 0.75
Identities = 11/80 (13%), Positives = 25/80 (31%), Gaps = 4/80 (5%)
Query: 24 PNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR----RGGVRLCRPADQITILDVV 79
P ++ +A L +L+ L + ++ G+ + P + L
Sbjct: 64 PKDLATLAADTGSVPPRLEMLLETLRQMRVINLEDGKWSLTEFADYMFSPTPKEPNLHQT 123
Query: 80 KATEESFFVAECFASHKIDC 99
+ F+A+ F
Sbjct: 124 PVAKAMAFLADDFYMGLSQA 143
>3e6c_C CPRK, cyclic nucleotide-binding protein; CPRK, halorespiration;
HET: DNA 3C4; 1.80A {Desulfitobacterium hafniense} SCOP:
a.4.5.4 b.82.3.2 PDB: 3e6b_A* 3e5u_C* 3e6d_A 3e5x_A*
3e5q_A 2h6b_A* 2h6c_A
Length = 250
Score = 28.0 bits (61), Expect = 0.83
Identities = 7/64 (10%), Positives = 21/64 (32%), Gaps = 12/64 (18%)
Query: 15 MYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQIT 74
+ P I E + + + ++L L + I++ + + I
Sbjct: 168 VGDTYEITMPLSQKSIGEITGVHHVTVSRVLASLKRENILDKKKNK------------II 215
Query: 75 ILDV 78
+ ++
Sbjct: 216 VYNL 219
>3jw4_A Transcriptional regulator, MARR/EMRR family; DNA-binding protein,
structural genomics, PSI-2, protein structure
initiative; HET: MSE; 2.10A {Clostridium acetobutylicum}
Length = 148
Score = 28.0 bits (62), Expect = 0.93
Identities = 14/91 (15%), Positives = 31/91 (34%), Gaps = 11/91 (12%)
Query: 8 DYGI-----RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR---- 58
+ G+ R++ Y + + +A+ + +LQ L K G +E
Sbjct: 36 ELGLNSQQGRMIGYIYENQESGIIQKDLAQFFGRRGASITSMLQGLEKKGYIERRIPENN 95
Query: 59 GRRGGVRLCRPADQI--TILDVVKATEESFF 87
R+ + + + ++ EES
Sbjct: 96 ARQKNIYVLPKGAALVEEFNNIFLEVEESIT 126
>2nu8_B SCS-beta, succinyl-COA synthetase beta chain; citric acid cycle,
heterotetramer, ligase, ATP-grAsp fold, rossmann fold;
HET: COA; 2.15A {Escherichia coli} SCOP: c.23.4.1
d.142.1.4 PDB: 1scu_B* 2nu6_B* 1jkj_B* 2nu7_B* 2nu9_B*
2nua_B* 2scu_B* 1jll_B* 1cqj_B* 1cqi_B*
Length = 388
Score = 27.7 bits (61), Expect = 0.97
Identities = 13/66 (19%), Positives = 21/66 (31%), Gaps = 10/66 (15%)
Query: 8 DYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLC 67
YG+ + A P + A VK + RG+ GGV++
Sbjct: 14 RYGLPAPVGYACTT--PREAEEAASKIGAGPWV--------VKCQVHAGGRGKAGGVKVV 63
Query: 68 RPADQI 73
+ I
Sbjct: 64 NSKEDI 69
>1zyb_A Transcription regulator, CRP family; NP_813211.1, structural
genomics, joint center for structural genomics, JCSG;
2.15A {Bacteroides thetaiotaomicron vpi-5482} SCOP:
a.4.5.4 b.82.3.2
Length = 232
Score = 27.7 bits (60), Expect = 1.0
Identities = 12/78 (15%), Positives = 23/78 (29%), Gaps = 12/78 (15%)
Query: 1 MHLTKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60
+K + + + ++ +A + L + K L L G++E R
Sbjct: 163 DLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCLDDTRLNISKTLNELQDNGLIELHRKE 222
Query: 61 RGGVRLCRPADQITILDV 78
I I D
Sbjct: 223 ------------ILIPDA 228
>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB:
2quf_A
Length = 232
Score = 27.3 bits (60), Expect = 1.4
Identities = 8/55 (14%), Positives = 22/55 (40%), Gaps = 3/55 (5%)
Query: 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR--GRRGG 63
+R + + S ++ +S + K L+ + + G++++ R G
Sbjct: 13 VRRDLLSHLTCM-ECYFSLLSSKVSVSSTAVAKHLKIMEREGVLQSYEKEERFIG 66
>3dp7_A SAM-dependent methyltransferase; structural genomics, protein
structure initiative, NEW YORK structural genomix
research, nysgxrc; 2.33A {Bacteroides vulgatus atcc
8482}
Length = 363
Score = 27.1 bits (59), Expect = 1.4
Identities = 4/34 (11%), Positives = 13/34 (38%)
Query: 27 ISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60
+ +I+ ++ +L+ + G + R
Sbjct: 53 LQEISGRTGLTRYAAQVLLEASLTIGTILLEEDR 86
>3deu_A Transcriptional regulator SLYA; MARR, WING-helix, transcription
regulator, activator, DNA-binding, repressor; HET: SAL;
2.30A {Salmonella typhimurium} SCOP: a.4.5.28
Length = 166
Score = 27.2 bits (60), Expect = 1.6
Identities = 14/91 (15%), Positives = 28/91 (30%), Gaps = 12/91 (13%)
Query: 8 DYGI-----RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR---- 58
+ L Q+A+A I + L + L L G++
Sbjct: 48 PLELTQTHWVTLHNIHQLPP-DQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCASD 106
Query: 59 GRRGGVRLCRPADQI--TILDVVKATEESFF 87
R ++L A+ + + +V+ T
Sbjct: 107 RRAKRIKLTEKAEPLIAEMEEVIHKTRGEIL 137
>1uw4_B UPF2, regulator of nonsense transcripts 2; nonsense mediated mRNA
decay protein, RNA-binding protein, NMD, RNP domain,
MIF4G domain; 1.95A {Homo sapiens} SCOP: a.118.1.14
Length = 248
Score = 26.9 bits (59), Expect = 1.9
Identities = 19/134 (14%), Positives = 38/134 (28%), Gaps = 17/134 (12%)
Query: 8 DYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLC 67
D + + N +I+ A + EL+ +++++ V I T+
Sbjct: 80 DGVLEDIRLGMEVNQPKFNQRRISSAKFLGELYNYRMVESAV---IFRTLY-----SFTS 131
Query: 68 RPADQITILDVVKATEESFFVAECFASHKIDCPLVGSCG--LTSVLRKALNAFFDVLTQY 125
+ + E F + C ++ +CG K F V Q
Sbjct: 132 FGVNPDGSPSSLDPPEHLFRI-RLV------CTILDTCGQYFDRGSSKRKLDCFLVYFQR 184
Query: 126 SIECLVRNRSSIKK 139
+ K
Sbjct: 185 YVWWKKSLEVWTKD 198
>3dv8_A Transcriptional regulator, CRP/FNR family; RER070207001219,
structural genomics, joint center for structural
genomics, JCSG; 2.55A {Eubacterium rectale atcc 33656}
Length = 220
Score = 26.6 bits (57), Expect = 2.4
Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 12/58 (20%)
Query: 20 HNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILD 77
N+ IA + ++L+ G+V+ RG+ ITILD
Sbjct: 165 TNELKITHETIANHLGSHREVITRMLRYFQVEGLVKLSRGK------------ITILD 210
>1ldj_A Cullin homolog 1, CUL-1; cullin, ROC1, HRT1, zinc ring finger,
ligase, ubiquitin, ubiquitination, SCF; 3.00A {Homo
sapiens} SCOP: a.4.5.34 a.118.17.1 e.40.1.1 PDB: 1u6g_A
1ldk_A 1ldk_B
Length = 760
Score = 26.2 bits (57), Expect = 2.6
Identities = 9/45 (20%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 9 YGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGI 53
+ + +L+ + Y + Q+ ++ I L ++LQ L+K+ +
Sbjct: 590 FQMAILLQYNTEDAY--TVQQLTDSTQIKMDILAQVLQILLKSKL 632
>2gau_A Transcriptional regulator, CRP/FNR family; structural genomics,
PSI; 1.90A {Porphyromonas gingivalis W83} SCOP: a.4.5.4
b.82.3.2
Length = 232
Score = 26.2 bits (56), Expect = 2.6
Identities = 7/64 (10%), Positives = 15/64 (23%), Gaps = 12/64 (18%)
Query: 15 MYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQIT 74
++A ++ + L V ++ R I
Sbjct: 171 ENDGATLSIYLSREELATLSNMTVSNAIRTLSTFVSERMLALDGKR------------IK 218
Query: 75 ILDV 78
I+D
Sbjct: 219 IIDC 222
>2frh_A SARA, staphylococcal accessory regulator A; winged-helix protein,
divalent metal binding, transcription; 2.50A
{Staphylococcus aureus} SCOP: a.4.5.28 PDB: 2fnp_A
1fzp_D
Length = 127
Score = 26.2 bits (57), Expect = 2.8
Identities = 7/57 (12%), Positives = 18/57 (31%)
Query: 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLC 67
VL Y + + + + I + + K ++ L + + R +
Sbjct: 40 FAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKRNEHDERTVL 96
>3lst_A CALO1 methyltransferase; calicheamicin, enediyne, SAH, structural
genomics, PSI-2, protein structure initiative; HET:
SAH; 2.40A {Micromonospora echinospora}
Length = 348
Score = 26.2 bits (57), Expect = 3.0
Identities = 9/37 (24%), Positives = 16/37 (43%)
Query: 24 PNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60
P +++A A L ++L+ L +V GR
Sbjct: 55 PRTPAELAAATGTDADALRRVLRLLAVRDVVRESDGR 91
>3nqo_A MARR-family transcriptional regulator; structural genomics, joint
center for structural genomics, J protein structure
initiative, PSI-2; HET: MSE PG4; 2.20A {Clostridium
difficile}
Length = 189
Score = 26.0 bits (57), Expect = 3.2
Identities = 7/44 (15%), Positives = 18/44 (40%)
Query: 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVE 55
++ + ++ IA S+ + +++ L K G V+
Sbjct: 45 MTILSILHLPEEETTLNNIARKMGTSKQNINRLVANLEKNGYVD 88
>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene
regulation; NMR {Streptomyces} SCOP: a.4.5.6
Length = 102
Score = 26.0 bits (57), Expect = 3.4
Identities = 11/57 (19%), Positives = 22/57 (38%), Gaps = 2/57 (3%)
Query: 29 QIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEES 85
I ++ + + L L G+V + G + + IT D +K E++
Sbjct: 40 DIRAQFGVAAKTVSRALAVLKSEGLVSSRGAL--GTVVEKNPIVITGADRLKRMEKN 94
>2fmy_A COOA, carbon monoxide oxidation system transcription regulator
COOA-1; DNA transcription regulator, DNA binding
protein; HET: HEM; 2.20A {Carboxydothermus
hydrogenoformans} PDB: 2hkx_A*
Length = 220
Score = 25.8 bits (55), Expect = 3.5
Identities = 11/60 (18%), Positives = 20/60 (33%), Gaps = 11/60 (18%)
Query: 19 IHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDV 78
I + +IA + + +L K GI+E V R + + D+
Sbjct: 162 IKLELGLNTEEIALMLGTTRQTVSVLLNDFKKMGILERVNQRT-----------LLLKDL 210
>3la7_A Global nitrogen regulator; activator, DNA-binding, transcription,
transcription regulation; HET: BOG; 1.90A {Anabaena}
PDB: 3la2_A* 3la3_A* 2xko_A* 2xgx_A* 2xhk_A* 2xkp_A*
Length = 243
Score = 25.9 bits (56), Expect = 3.6
Identities = 10/63 (15%), Positives = 21/63 (33%), Gaps = 12/63 (19%)
Query: 15 MYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQIT 74
I D IAEA + + + ++L L + ++ + + IT
Sbjct: 184 CADGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLREKKMISIHKKK------------IT 231
Query: 75 ILD 77
+
Sbjct: 232 VHK 234
>2p4w_A Transcriptional regulatory protein ARSR family; archaea, PHR,
heat shock, transcriptional regulation, winged helix,
DNA binding; 2.60A {Pyrococcus furiosus} SCOP: a.4.5.64
Length = 202
Score = 25.8 bits (56), Expect = 3.9
Identities = 8/52 (15%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRG 62
R + + P +S+++ + + + + L+ L +AG++E+ +
Sbjct: 16 TRRRILFLLTKR-PYFVSELSRELGVGQKAVLEHLRILEEAGLIESRVEKIP 66
>1fui_A L-fucose isomerase; ketol isomerase, fucose metabolism, L-fucose
to L-fuculose conversion; HET: FOC; 2.50A {Escherichia
coli K12} SCOP: b.43.2.1 c.85.1.1
Length = 591
Score = 25.7 bits (56), Expect = 3.9
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 48 LVKAGIVETVRGRRGGVR 65
L K GI + GRR GVR
Sbjct: 6 LPKIGIRPVIDGRRMGVR 23
>3gwz_A MMCR; methyltransferase, mitomycin, S-adenosyl methionine,
transferase; HET: MSE SAH; 1.91A {Streptomyces
lavendulae} PDB: 3gxo_A*
Length = 369
Score = 25.4 bits (55), Expect = 4.5
Identities = 9/38 (23%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 18 AIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVE 55
+ + P + +AEA E L ++L+ L G+ +
Sbjct: 66 LLQ-EGPRTATALAEATGAHEQTLRRLLRLLATVGVFD 102
>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary
phase, DNA-binding, transcription regulation; 1.50A
{Thermus thermophilus}
Length = 202
Score = 25.3 bits (54), Expect = 4.9
Identities = 9/64 (14%), Positives = 20/64 (31%), Gaps = 12/64 (18%)
Query: 15 MYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQIT 74
++A A + K++ L + G + + G+ I
Sbjct: 137 HEEEGKVVLKATHDELAAAVGSVRETVTKVIGELAREGYIRSGYGK------------IQ 184
Query: 75 ILDV 78
+LD+
Sbjct: 185 LLDL 188
>1u2w_A CADC repressor, cadmium efflux system accessory protein; zinc,
LEAD, SOFT metal ION resistance, ARSR/SMTB family, DNA
binding protein; 1.90A {Staphylococcus aureus} SCOP:
a.4.5.5 PDB: 3f72_A
Length = 122
Score = 25.2 bits (55), Expect = 5.3
Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 2/62 (3%)
Query: 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPA 70
R + A+ D + IA ++ L+ L K G+V + G + L
Sbjct: 43 NRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFR--KEGKLALYSLG 100
Query: 71 DQ 72
D+
Sbjct: 101 DE 102
>3kcc_A Catabolite gene activator; helix-turn-helix, CAMP, CAMP-binding,
DNA- binding, nucleotide-binding, transcription; HET:
CMP; 1.66A {Escherichia coli k-12} PDB: 3fwe_A 1g6n_A*
2cgp_A* 3hif_A 1i5z_A* 1j59_A* 1lb2_A* 1run_A* 1zrc_A*
1zrd_A* 1zre_A* 1zrf_A* 2gzw_A* 2wc2_A 3iyd_G* 1hw5_A*
1ruo_A* 1i6x_A* 1cgp_A* 1o3t_A* ...
Length = 260
Score = 25.3 bits (54), Expect = 5.7
Identities = 10/83 (12%), Positives = 24/83 (28%), Gaps = 18/83 (21%)
Query: 1 MHLTKRTDYGIRVLMYCAIHNDYPNRIS------QIAEACCISELFLFKILQPLVKAGIV 54
+ +T R + L +P+ + +I + S + +IL+ L ++
Sbjct: 188 LLVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLI 247
Query: 55 ETVRGRRGGVRLCRPADQITILD 77
I +
Sbjct: 248 SAHGKT------------IVVYG 258
>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural
genomics, protein structure initiativ midwest center
for structural genomics; 2.15A {Escherichia coli}
Length = 120
Score = 25.1 bits (55), Expect = 5.7
Identities = 10/38 (26%), Positives = 17/38 (44%), Gaps = 4/38 (10%)
Query: 12 RVLMYCAIHNDYPNRIS--QIAEACCISELFLFKILQP 47
RV I+N+ + + +IA +S L K L+
Sbjct: 11 RVCTV--INNNIAHEWTLARIASELLMSPSLLKKKLRE 46
>3cuo_A Uncharacterized HTH-type transcriptional regulator YGAV;
DNA-binding transcriptional regulator, structural
genomics, PSI, MCSG; 2.00A {Escherichia coli K12}
Length = 99
Score = 25.2 bits (55), Expect = 5.8
Identities = 8/76 (10%), Positives = 27/76 (35%), Gaps = 3/76 (3%)
Query: 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPA 70
R+L+ C + ++ +S + L + G++++ R L
Sbjct: 25 KRLLILCMLSGSPGTSAGELTRITGLSASATSQHLARMRDEGLIDSQ--RDAQRILYSIK 82
Query: 71 DQITILDVVKATEESF 86
++ + ++ + +
Sbjct: 83 NE-AVNAIIATLKNVY 97
>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX,
paired domain, DNA-binding protein, gene regulation/DNA
complex; HET: DNA; 2.50A {Drosophila melanogaster}
SCOP: a.4.1.5
Length = 128
Score = 25.2 bits (55), Expect = 6.3
Identities = 10/56 (17%), Positives = 19/56 (33%)
Query: 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVK 80
R I+ +S + KIL + G + R+ P + I + +
Sbjct: 34 IRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYKR 89
>3a9s_A D-arabinose isomerase; rossmann fold, beta barrel, carbohydrate
metabolism, cytoplasm, fucose metabolism, manganese,
metal- binding; 1.60A {Geobacillus pallidus} PDB:
3a9r_A 3a9t_A*
Length = 595
Score = 25.2 bits (54), Expect = 6.4
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 48 LVKAGIVETVRGRRGGVR 65
L K GI T+ GRR GVR
Sbjct: 11 LPKIGIRPTIDGRRKGVR 28
>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix,
homodimer, transcription regulator; 3.60A {Pseudomonas
aeruginosa}
Length = 227
Score = 25.0 bits (53), Expect = 6.6
Identities = 11/63 (17%), Positives = 17/63 (26%), Gaps = 12/63 (19%)
Query: 16 YCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITI 75
+ P +A I +I+ L GI+ I+I
Sbjct: 170 GENCRVEIPVAKQLVAGHLSIQPETFSRIMHRLGDEGIIHLDGRE------------ISI 217
Query: 76 LDV 78
LD
Sbjct: 218 LDR 220
>2zdb_A Transcriptional regulator, CRP family; CAMP-binding domain, winged
helix-turn-helix, thermus thermophilus DNA-binding,
plasmid; 2.00A {Thermus thermophilus}
Length = 195
Score = 24.8 bits (53), Expect = 6.7
Identities = 11/64 (17%), Positives = 21/64 (32%), Gaps = 12/64 (18%)
Query: 15 MYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQIT 74
+IA+A + K+L L + G++ T R +
Sbjct: 130 ARDRQGIYVTVSHEEIADATASIRESVSKVLADLRREGLIATAYRR------------VY 177
Query: 75 ILDV 78
+LD+
Sbjct: 178 LLDL 181
>2ek5_A Predicted transcriptional regulators; helix-turn-helix,
interwined alpha helices; 2.20A {Corynebacterium
glutamicum atcc 13032} PDB: 2du9_A
Length = 129
Score = 24.6 bits (53), Expect = 7.7
Identities = 15/56 (26%), Positives = 20/56 (35%)
Query: 29 QIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEE 84
++A I+ L LV+AGI+ RG V PA D A
Sbjct: 33 ELAAFHRINPATARNGLTLLVEAGILYKKRGIGMFVSAQAPALIRERRDAAFAATY 88
>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure
initiative, MI center for structural genomics, MCSG,
unknown function; 1.58A {Listeria innocua}
Length = 125
Score = 24.8 bits (54), Expect = 8.8
Identities = 11/60 (18%), Positives = 22/60 (36%), Gaps = 4/60 (6%)
Query: 29 QIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITIL--DVVKATEESF 86
++ ++ + + Q L +AG + RG G + L ++ A E F
Sbjct: 42 EMGVKLAVNPNTVSRAYQELERAGYIYAKRGM--GSFVTSDKALFDQLKKELADAITERF 99
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
0.329 0.141 0.428
Gapped
Lambda K H
0.267 0.0589 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,178,701
Number of extensions: 49045
Number of successful extensions: 237
Number of sequences better than 10.0: 1
Number of HSP's gapped: 229
Number of HSP's successfully gapped: 67
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: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 52 (24.1 bits)