RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780444|ref|YP_003064857.1| bacteriophage repressor
protein C1 [Candidatus Liberibacter asiaticus str. psy62]
(223 letters)
>2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity,
transcription regulator; 1.95A {Enterobacteria phage
186} PDB: 2fkd_A
Length = 189
Score = 45.1 bits (106), Expect = 1e-05
Identities = 25/213 (11%), Positives = 55/213 (25%), Gaps = 41/213 (19%)
Query: 11 EAIDRMAERHNL-TPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETI 69
+ +DR+ E + LA + +S + G + ET
Sbjct: 9 DVLDRICEAYGFSQKIQLANHFDIASSSLSNRYTRGAISYD---------FAAHCALETG 59
Query: 70 CQLLDLPFSDGRTTEKKEKEIPLLYFP--PSGSGGFFDSGVFPTGNKWNTVGVPEIRSPH 127
L L +G + ++ T +
Sbjct: 60 ANLQWLLTGEGEAFVNNRESSDAKRIEGFTLSEEILKSDKQLSVDAQFFTKPL------- 112
Query: 128 NGIYAIQTQDTRHKTQDTSMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLIS 187
T + + +G I ++ ++ G L+ I + L
Sbjct: 113 -----------------TDGMAIRSEGKIYFVDKQASLSDGLWLVDIKGAISI--RELTK 153
Query: 188 RRGRSIDLMSLNCCYPVDTVEMSDIEWIARILW 220
GR + + + + DI+ + R++
Sbjct: 154 LPGRKLHVAGGKVPFE---CGIDDIKTLGRVVG 183
>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A
{Enterobacteria phage lambda}
Length = 236
Score = 38.9 bits (89), Expect = 8e-04
Identities = 22/224 (9%), Positives = 62/224 (27%), Gaps = 20/224 (8%)
Query: 7 KKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATN 66
+++ ++ L+ +A K G+ + + + + +
Sbjct: 16 RRLKAIYEKKKNELGLSQESVADKMGMGQSGVGA-----LFNGINALNAYNAALLAKILK 70
Query: 67 ETICQLLDLPFSDGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIRSP 126
++ + + E + + G +
Sbjct: 71 VSVEE----FSPSIAREIYEMYEAVSMQPSLRSEYEYPVFSHVQAGMFSPELRTFTKGDA 126
Query: 127 HNGIYAIQTQDTRH---KTQDTSML------PLYRKGDILILNSAIQVNCGDRLLIKPRT 177
+ + + + SM P + G +++++ V GD + +
Sbjct: 127 ERWVSTTKKASDSAFWLEVEGNSMTAPTGSKPSFPDGMLILVDPEQAVEPGDFCIARLGG 186
Query: 178 GDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMSDIEWIARILWA 221
+ K LI R + L LN YP+ + +++ +
Sbjct: 187 DEFTFKKLI-RGSGQVFLQPLNPQYPMIPCN-ESCSVVGKVIAS 228
>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 = 37.4 bits (86), Expect = 0.003
Identities = 15/95 (15%), Positives = 41/95 (43%), Gaps = 5/95 (5%)
Query: 4 FSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILA 63
+ + + AI ++ LT + +DP IE + + PS + ++ +++
Sbjct: 8 YDFRALGLAIKEARKKQGLTREQVGAMIEIDPRYLTN-----IENKGQHPSLQVLYDLVS 62
Query: 64 ATNETICQLLDLPFSDGRTTEKKEKEIPLLYFPPS 98
N ++ + S ++T++++ E + F +
Sbjct: 63 LLNVSVDEFFLPASSQVKSTKRRQLENKIDNFTDA 97
>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus
caldolyticus} SCOP: a.35.1.3
Length = 77
Score = 35.1 bits (81), Expect = 0.012
Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 5/69 (7%)
Query: 6 HKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAAT 65
+K + ++ + ++ LA AGL T ++ +E +R S +I KI AA
Sbjct: 8 KRKFGRTLKKIRTQKGVSQEELADLAGLHRTYISE-----VERGDRNISLINIHKICAAL 62
Query: 66 NETICQLLD 74
+
Sbjct: 63 DIPASTFFR 71
>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein
fold, OPPF, structural genomics, oxford protein
production facility; 2.80A {Neisseria gonorrhoeae}
Length = 141
Score = 34.5 bits (79), Expect = 0.020
Identities = 13/67 (19%), Positives = 25/67 (37%), Gaps = 5/67 (7%)
Query: 7 KKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATN 66
K E + + T S LA AGL ++ IE + +++ K+ A
Sbjct: 67 KAGGETFVSLRMKKGFTQSELATAAGLPQPYLSR-----IENSKQSLQDKTVQKLANALG 121
Query: 67 ETICQLL 73
+ ++
Sbjct: 122 VSPLEVR 128
>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 = 33.3 bits (76), Expect = 0.045
Identities = 11/85 (12%), Positives = 27/85 (31%), Gaps = 5/85 (5%)
Query: 6 HKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAAT 65
+ E + R+ + H L +A + + P E + ++
Sbjct: 7 QHQFAENLSRLKKEHGLKNHQIAELLNVQTRTVAY-----YMSGETKPDIEKLIRLATYF 61
Query: 66 NETICQLLDLPFSDGRTTEKKEKEI 90
+ +I +L+ D + K+
Sbjct: 62 HLSIDELVGYVQEDKVWNDLSLKQW 86
>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 = 32.1 bits (73), Expect = 0.11
Identities = 14/65 (21%), Positives = 25/65 (38%), Gaps = 5/65 (7%)
Query: 8 KIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNE 67
K + + + L+ LA +GLD + +E R S +I K+ A +
Sbjct: 13 KFGQRLRELRTAKGLSQETLAFLSGLDRSYVGG-----VERGQRNVSLVNILKLATALDI 67
Query: 68 TICQL 72
+L
Sbjct: 68 EPREL 72
>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 = 31.9 bits (72), Expect = 0.11
Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 5/75 (6%)
Query: 1 MTSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFK 60
M SF K+ I ++ +T LA K+ LD T + IE +R + +S+
Sbjct: 4 MESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISG-----IERNSRNLTIKSLEL 58
Query: 61 ILAATNETICQLLDL 75
I+ + ++
Sbjct: 59 IMKGLEVSDVVFFEM 73
>2p5t_A Putative transcriptional regulator PEZA; postsegregational
killing system, phosphoryltransferase, helix-turn-helix
motif, transcription regulator; 3.20A {Streptococcus
pneumoniae TIGR4}
Length = 158
Score = 31.6 bits (71), Expect = 0.16
Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 5/63 (7%)
Query: 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETIC 70
+ I + + H+LT AR G+ S ++ E STE I I N +
Sbjct: 4 KNIKSLRKTHDLTQLEFARIVGISRNSLSR-----YENGTSSVSTELIDIICQKFNVSYV 58
Query: 71 QLL 73
++
Sbjct: 59 DIV 61
>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 = 30.5 bits (69), Expect = 0.31
Identities = 10/64 (15%), Positives = 24/64 (37%), Gaps = 6/64 (9%)
Query: 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETIC 70
+ + L + LA+K G S + +E + + ++ +A ++
Sbjct: 4 SRVKSKRIQLGLNQAELAQKVGTTQQSIEQ-----LE-NGKTKRPRFLPELASALGVSVD 57
Query: 71 QLLD 74
LL+
Sbjct: 58 WLLN 61
>1y4w_A EXO-inulinase; glycoside hydrolase family 32, crystallographic
structure, native structure; HET: NAG; 1.55A
{Aspergillus awamori} SCOP: b.29.1.19 b.67.2.3 PDB:
1y9g_A* 1y9m_A*
Length = 518
Score = 29.5 bits (65), Expect = 0.59
Identities = 9/47 (19%), Positives = 16/47 (34%)
Query: 70 CQLLDLPFSDGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWN 116
Q + DG T + P++ PPS + + P +
Sbjct: 131 SQSIAYSLDDGLTWTTYDAANPVIPNPPSPYEAEYQNFRDPFVFWHD 177
>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein
structure initiative, MI center for structural
genomics, MCSG; 1.65A {Cytophaga hutchinsonii}
Length = 73
Score = 29.0 bits (65), Expect = 0.94
Identities = 14/69 (20%), Positives = 28/69 (40%), Gaps = 5/69 (7%)
Query: 5 SHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAA 64
+ +KI+ + + T L + T+ +K + PS E++F I A
Sbjct: 5 TERKIFNRLKSVLAEKGKTNLWLTETLDKNKTTVSK-----WCTNDVQPSLETLFDIAEA 59
Query: 65 TNETICQLL 73
N + +L+
Sbjct: 60 LNVDVRELI 68
>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein
structure initiative, midwest center for structural
genomics; 2.00A {Lactobacillus plantarum WCFS1}
Length = 78
Score = 28.8 bits (64), Expect = 1.1
Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 5/76 (6%)
Query: 1 MTSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFK 60
M + + + E + + + NLT + +A AGL+ ++ N R++ P+ +I K
Sbjct: 1 MKTDG-EFVSEHLMELITQQNLTINRVATLAGLNQSTVNAMFEG----RSKRPTITTIRK 55
Query: 61 ILAATNETICQLLDLP 76
+ ++ D P
Sbjct: 56 VCGTLGISVHDFFDFP 71
>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 = 28.4 bits (63), Expect = 1.3
Identities = 12/63 (19%), Positives = 22/63 (34%), Gaps = 5/63 (7%)
Query: 13 IDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQL 72
+ + E+ ++ S LA + + N IE PS + KI N + +
Sbjct: 6 LKLIREKKKISQSELAALLEVSRQTING-----IEKNKYNPSLQLALKIAYYLNTPLEDI 60
Query: 73 LDL 75
Sbjct: 61 FQW 63
>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 = 28.4 bits (63), Expect = 1.4
Identities = 4/68 (5%), Positives = 20/68 (29%), Gaps = 5/68 (7%)
Query: 7 KKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATN 66
+++ ++ L+ +A K G+ + + + + +
Sbjct: 16 RRLKAIYEKKKNELGLSQESVADKMGMGQSGVGA-----LFNGINALNAYNAALLAKILK 70
Query: 67 ETICQLLD 74
++ +
Sbjct: 71 VSVEEFSP 78
>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing
proteins); PSI-2, midwest center for structural
genomics; 1.65A {Chromobacterium violaceum}
Length = 113
Score = 28.1 bits (63), Expect = 1.5
Identities = 8/38 (21%), Positives = 14/38 (36%), Gaps = 2/38 (5%)
Query: 5 SHKKIWEAIDRMAER--HNLTPSGLARKAGLDPTSFNK 40
S K+ EA+ M L+ +A G+ +
Sbjct: 5 SQPKLTEAVSLMEANIEEPLSTDDIAYYVGVSRRQLER 42
>2dig_A Lamin-B receptor; tudor domain, integral nuclear envelope inner
membrane protein, nuclear protein, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: b.34.9.1
Length = 68
Score = 27.6 bits (61), Expect = 2.1
Identities = 16/65 (24%), Positives = 30/65 (46%), Gaps = 4/65 (6%)
Query: 26 GLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPFSDGRTTEK 85
G + +G+ F G R RWP + +++ ++++ QL + + DG E
Sbjct: 1 GSSGSSGMPSRKFAD----GEVVRGRWPGSSLYYEVEILSHDSTSQLYTVKYKDGTELEL 56
Query: 86 KEKEI 90
KE +I
Sbjct: 57 KENDI 61
>3kwo_A Putative bacterioferritin; alpha-helix, bacterial ferritin fold,
structural genomics, center for structural genomics of
infectious diseases; 1.99A {Campylobacter jejuni}
Length = 152
Score = 27.2 bits (60), Expect = 3.1
Identities = 11/65 (16%), Positives = 22/65 (33%), Gaps = 5/65 (7%)
Query: 9 IWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNET 68
+ E D AER L KA ++ + ++ + E I +++ E
Sbjct: 50 MAELFDSCAERVL----QLGEKAITCQKVLMENAKSPKVAKDCFTPLEVI-ELIKQDYEY 104
Query: 69 ICQLL 73
+
Sbjct: 105 LLAEF 109
>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 = 27.2 bits (59), Expect = 3.3
Identities = 9/68 (13%), Positives = 23/68 (33%), Gaps = 5/68 (7%)
Query: 7 KKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATN 66
+I + + + L+ A+ G+ + IE P+ +++KI +
Sbjct: 10 SQIANQLKNLRKSRGLSLDATAQLTGVSKAMLGQ-----IERGESSPTIATLWKIASGLE 64
Query: 67 ETICQLLD 74
+
Sbjct: 65 ASFSAFFA 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 = 26.8 bits (59), Expect = 3.8
Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 7/76 (9%)
Query: 1 MTSFSHKKIW-EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIF 59
M S + + + E I ++ ++ +LT + G +F++ E N P S
Sbjct: 3 MASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSR-----YEKGNAXPH-PSTI 56
Query: 60 KILAATNETICQLLDL 75
K+L ++ L ++
Sbjct: 57 KLLRVLDKHPELLNEI 72
>1jhf_A LEXA repressor; LEXA SOS repressor, hydrolase; 1.80A {Escherichia
coli} SCOP: a.4.5.2 b.87.1.1 PDB: 1jhh_A 1jhc_A 1jhe_A
1lea_A 1leb_A
Length = 202
Score = 26.6 bits (58), Expect = 4.2
Identities = 25/210 (11%), Positives = 67/210 (31%), Gaps = 36/210 (17%)
Query: 7 KKIWEAIDRMAERHNLTPS--GLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAA 64
+++++ I + + P+ +A++ G S + + L A
Sbjct: 9 QEVFDLIRDHISQTGMPPTRAEIAQRLGFR-------------------SPNAAEEHLKA 49
Query: 65 TNETICQLLDLPFSDGRT-TEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEI 123
+ S G +++E+ +PL+ + + V
Sbjct: 50 LARKGVIEIVSGASRGIRLLQEEEEGLPLVGRVAADEPLLAQQ------HIEGHYQVDPS 103
Query: 124 RSPHNGIYAIQTQDTRHKTQDTSMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAK 183
N + ++ + GD+L ++ V G ++ + ++ K
Sbjct: 104 LFKPNADFLLRVSG------MSMKDIGIMDGDLLAVHKTQDVRNGQVVVAR-IDDEVTVK 156
Query: 184 VLISRRGRSIDLMSLNCCYPVDTVEMSDIE 213
L ++G ++L+ N + V++
Sbjct: 157 RLK-KQGNKVELLPENSEFKPIVVDLRQQS 185
>3kdp_B Sodium/potassium-transporting ATPase subunit beta-1; alpha helical,
heterotrimeric membrane protein complex, ATP- binding,
hydrolase, ION transport; HET: CLR; 3.50A {Sus scrofa}
Length = 286
Score = 26.5 bits (58), Expect = 5.0
Identities = 12/41 (29%), Positives = 15/41 (36%), Gaps = 1/41 (2%)
Query: 79 DGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVG 119
G+ E KEK + YF G G F +P K
Sbjct: 197 TGKRDEDKEKVGTMEYFGLGGYPG-FPLQYYPYYGKLLQPK 236
>2iny_A Hexon protein, late protein 2; avian adenovirus, CELO, major coat
protein, crystal packing, nanotechnology, viral jelly
roll, viral protein; 3.90A {Fowl adenovirus 1}
Length = 942
Score = 26.2 bits (58), Expect = 6.2
Identities = 11/33 (33%), Positives = 15/33 (45%)
Query: 87 EKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVG 119
E+ +P F P G G D+G + K T G
Sbjct: 371 EEGVPTYAFLPDGHGAGEDNGPDLSNVKIYTNG 403
>2obe_A Hexon, PII; trimer, double-barrel subunit, viral jellyroll, base,
hypervariable tower, viral protein; 2.10A {Simian
adenovirus 25} PDB: 1p2z_A* 1p30_A 2bvi_F
Length = 932
Score = 25.8 bits (57), Expect = 7.3
Identities = 9/32 (28%), Positives = 11/32 (34%), Gaps = 1/32 (3%)
Query: 87 EKEIPLLYFPPSGSG-GFFDSGVFPTGNKWNT 117
E E+P FP G G+ G T
Sbjct: 388 EDELPNYCFPLDAVGRTDTYQGIKANGTDQTT 419
>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 = 25.7 bits (56), Expect = 8.5
Identities = 14/74 (18%), Positives = 32/74 (43%), Gaps = 5/74 (6%)
Query: 6 HKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAAT 65
++ + + + ++ + +L+ S LA GL + +K IE R +F++L
Sbjct: 8 YRCLVQLLTKLRKEASLSQSELAIFLGLSQSDISK-----IESFERRLDALELFELLEVV 62
Query: 66 NETICQLLDLPFSD 79
+ +D+ D
Sbjct: 63 ASRLGLPMDILLKD 76
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 0.136 0.418
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: 2,002,709
Number of extensions: 88717
Number of successful extensions: 300
Number of sequences better than 10.0: 1
Number of HSP's gapped: 297
Number of HSP's successfully gapped: 28
Length of query: 223
Length of database: 5,693,230
Length adjustment: 89
Effective length of query: 134
Effective length of database: 3,535,514
Effective search space: 473758876
Effective search space used: 473758876
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: 55 (25.2 bits)