RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16245
(113 letters)
>2ebl_A COUP transcription factor 1; DNA-binding, metal-binding, nuclear
protein, receptor, transcription regulation, zinc, EAR3,
erbal3 tfcoup1; NMR {Homo sapiens}
Length = 89
Score = 117 bits (296), Expect = 3e-36
Identities = 42/76 (55%), Positives = 53/76 (69%), Gaps = 4/76 (5%)
Query: 38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQC 97
I C VCGD+SSGKHYG ++C+GC FFKRS+ RN YTC+A + CPID+ HRNQC
Sbjct: 7 GIECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRN----CPIDQHHRNQC 62
Query: 98 RACRLNKCFMSAMNKD 113
+ CRL KC M ++
Sbjct: 63 QYCRLKKCLKVGMRRE 78
>3cbb_A HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DNA binding domain,
nuclear; zinc finger; 2.00A {Homo sapiens}
Length = 78
Score = 112 bits (283), Expect = 2e-34
Identities = 39/73 (53%), Positives = 51/73 (69%), Gaps = 4/73 (5%)
Query: 41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
C +CGDR++GKHYG SCDGC GFF+RS+ +N +Y+C+ C +DK RNQCR C
Sbjct: 3 CAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQ----CVVDKDKRNQCRYC 58
Query: 101 RLNKCFMSAMNKD 113
RL KCF + M K+
Sbjct: 59 RLKKCFRAGMKKE 71
>1ynw_B Retinoic acid receptor RXR-alpha, retinoid X receptor; VDR, nuclear
receptor, protein-DNA complex, transcripti complex;
3.00A {Homo sapiens} SCOP: g.39.1.2
Length = 99
Score = 112 bits (283), Expect = 4e-34
Identities = 38/73 (52%), Positives = 50/73 (68%), Gaps = 4/73 (5%)
Query: 41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
C +CGDRSSGKHYG+YSC+GC GFFKR++ ++ YTC+ D C IDK RN+C+ C
Sbjct: 6 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKD----CLIDKRQRNRCQYC 61
Query: 101 RLNKCFMSAMNKD 113
R KC M ++
Sbjct: 62 RYQKCLAMGMKRE 74
>1dsz_A RAR-alpha, retinoic acid receptor alpha; RAR, nuclear receptor,
protein-DNA, transcription/DNA complex; HET: DNA; 1.70A
{Homo sapiens} SCOP: g.39.1.2 PDB: 1hra_A
Length = 86
Score = 112 bits (281), Expect = 5e-34
Identities = 39/74 (52%), Positives = 51/74 (68%), Gaps = 4/74 (5%)
Query: 40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
PC VC D+SSG HYG+ +C+GC GFF+RSI +N VYTC + C I+K RN+C+
Sbjct: 6 PCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKN----CIINKVTRNRCQY 61
Query: 100 CRLNKCFMSAMNKD 113
CRL KCF M+K+
Sbjct: 62 CRLQKCFEVGMSKE 75
>2han_A Protein ultraspiracle; transcription regulation, transcription
factor, DNA-binding, nuclear protein, nuclear receptor,
zinc finger; 1.95A {Drosophila melanogaster} SCOP:
g.39.1.2
Length = 93
Score = 112 bits (281), Expect = 6e-34
Identities = 36/84 (42%), Positives = 50/84 (59%), Gaps = 4/84 (4%)
Query: 30 SASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPI 89
S C +CGDR+SGKHYG+YSC+GC GFFKR++ ++ Y C+ + C I
Sbjct: 2 SNHPLSGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRN----CII 57
Query: 90 DKTHRNQCRACRLNKCFMSAMNKD 113
DK RN+C+ CR KC M ++
Sbjct: 58 DKRQRNRCQYCRYQKCLTCGMKRE 81
>1dsz_B RXR-alpha, retinoic acid receptor RXR-alpha; RAR, nuclear receptor,
protein-DNA, transcription/DNA complex; HET: DNA; 1.70A
{Homo sapiens} SCOP: g.39.1.2 PDB: 1by4_A* 1rxr_A 1r0n_A
1r0o_A 2nll_A*
Length = 85
Score = 111 bits (279), Expect = 8e-34
Identities = 38/78 (48%), Positives = 50/78 (64%), Gaps = 4/78 (5%)
Query: 36 LLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRN 95
C +CGDRSSGKHYG+YSC+GC GFFKR++ ++ YTC+ D C IDK RN
Sbjct: 3 FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKD----CLIDKRQRN 58
Query: 96 QCRACRLNKCFMSAMNKD 113
+C+ CR KC M ++
Sbjct: 59 RCQYCRYQKCLAMGMKRE 76
>1a6y_A Orphan nuclear receptor NR1D1; orphan receptor, DNA-binding,
reverb, REV- ERB, transcription regulation,
transcription/DNA complex; HET: DNA 5IU; 2.30A {Homo
sapiens} SCOP: g.39.1.2 PDB: 1ga5_A* 1hlz_A
Length = 94
Score = 110 bits (278), Expect = 2e-33
Identities = 33/77 (42%), Positives = 49/77 (63%), Gaps = 3/77 (3%)
Query: 37 LDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQ 96
+ + CKVCGD +SG HYG+ +C+GC GFF+RSI +N Y + +C I + +RN+
Sbjct: 6 MVLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLK---NENCSIVRINRNR 62
Query: 97 CRACRLNKCFMSAMNKD 113
C+ CR KC M++D
Sbjct: 63 CQQCRFKKCLSVGMSRD 79
>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus
interaction, metal-binding, nucleus, receptor,
transcription, transcription regulation, zinc-FIN
activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB:
3dzu_A* 3e00_A*
Length = 467
Score = 119 bits (300), Expect = 2e-33
Identities = 40/102 (39%), Positives = 54/102 (52%), Gaps = 4/102 (3%)
Query: 12 PPRYPQYFMSRPDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHR 71
+ P S + C +CGDRSSGKHYG+YSC+GC GFFKR++ +
Sbjct: 111 DIKPPLGLNGVLKVPAHPSGNMASFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRK 170
Query: 72 NRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113
+ YTC+ D C IDK RN+C+ CR KC M ++
Sbjct: 171 DLTYTCRDNKD----CLIDKRQRNRCQYCRYQKCLAMGMKRE 208
>1hcq_A Protein (estrogen receptor); protein-DNA complex, complexed with
drug, transcription/DNA complex; HET: DNA; 2.40A {Homo
sapiens} SCOP: g.39.1.2 PDB: 1hcp_A 4aa6_A
Length = 84
Score = 107 bits (269), Expect = 3e-32
Identities = 36/76 (47%), Positives = 43/76 (56%), Gaps = 4/76 (5%)
Query: 38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQC 97
C VC D +SG HYG++SC+GC FFKRSI + Y C A C IDK R C
Sbjct: 4 TRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQ----CTIDKNRRKSC 59
Query: 98 RACRLNKCFMSAMNKD 113
+ACRL KC+ M K
Sbjct: 60 QACRLRKCYEVGMMKG 75
>3dzy_D Peroxisome proliferator-activated receptor gamma; DNA-binding,
HOST-virus interaction, metal-binding, nucleus,
receptor, transcription, transcription regulation,
zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo
sapiens} PDB: 3dzu_D* 3e00_D* 2env_A
Length = 419
Score = 115 bits (288), Expect = 6e-32
Identities = 35/108 (32%), Positives = 53/108 (49%), Gaps = 5/108 (4%)
Query: 6 GNCRQIPPRYPQYFMSRPDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFF 65
+ P P Y + L+ I C+VCGD++SG HYG+++C+GC GFF
Sbjct: 18 SAIKVEPASPPYYSEKTQLYNKPHEEPSNSLMAIECRVCGDKASGFHYGVHACEGCKGFF 77
Query: 66 KRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113
+R+I +Y +C I K RN+C+ CR KC M+ +
Sbjct: 78 RRTIRLKLIYDRCD-----LNCRIHKKSRNKCQYCRFQKCLAVGMSHN 120
>1cit_A NGFI-B, protein (orphan nuclear receptor NGFI-B); early immediate
response gene product, transcription factor, monomeric
protein-DNA complex; HET: DNA; 2.70A {Rattus norvegicus}
SCOP: g.39.1.2
Length = 89
Score = 104 bits (262), Expect = 4e-31
Identities = 34/73 (46%), Positives = 47/73 (64%), Gaps = 4/73 (5%)
Query: 41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
C VCGD +S +HYG+ +C+GC GFFKR++ ++ Y C A D CP+DK RN+C+ C
Sbjct: 3 CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKD----CPVDKRRRNRCQFC 58
Query: 101 RLNKCFMSAMNKD 113
R KC M K+
Sbjct: 59 RFQKCLAVGMVKE 71
>3g9m_A Glucocorticoid receptor; glucocorticoid, DNA-binding, allostery,
lever ARM, transcription, hormone; HET: DNA; 1.61A
{Rattus norvegicus} PDB: 3g6p_A* 3g6q_B* 3g6r_B* 3g6u_A*
3g8u_A* 3g8x_A* 3g97_B* 3g99_A* 3g9i_A* 3g9j_A* 3fyl_A*
3g9o_B* 3g9p_B* 3g6t_A* 1r4o_A 1r4r_A 1glu_A* 1gdc_A
2gda_A 1rgd_A ...
Length = 90
Score = 104 bits (260), Expect = 7e-31
Identities = 31/74 (41%), Positives = 39/74 (52%), Gaps = 4/74 (5%)
Query: 40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
C VC D +SG HYG+ +C C FFKR++ Y C + D C IDK R C A
Sbjct: 4 MCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRND----CIIDKIRRKNCPA 59
Query: 100 CRLNKCFMSAMNKD 113
CR KC + MN +
Sbjct: 60 CRYRKCLQAGMNLE 73
>2a66_A Orphan nuclear receptor NR5A2; protein-DNA complex, zinc finger,
DNA- binding domain, transcription factor, FTZ-F1,
C-terminal extension; 2.20A {Homo sapiens} PDB: 2ff0_A
Length = 113
Score = 104 bits (261), Expect = 1e-30
Identities = 35/80 (43%), Positives = 46/80 (57%), Gaps = 4/80 (5%)
Query: 34 DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTH 93
D L+ C VCGD+ SG HYG+ +C+ C GFFKR++ N+ YTC + C IDKT
Sbjct: 5 DEDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQN----CQIDKTQ 60
Query: 94 RNQCRACRLNKCFMSAMNKD 113
R +C CR KC M +
Sbjct: 61 RKRCPYCRFQKCLSVGMKLE 80
>1lo1_A Steroid hormone receptor ERR2; estrogen related receptor 2, DNA
binding domain, HERR2, hormone nuclear receptor; NMR
{Homo sapiens} SCOP: g.39.1.2
Length = 98
Score = 102 bits (257), Expect = 3e-30
Identities = 33/74 (44%), Positives = 41/74 (55%), Gaps = 4/74 (5%)
Query: 40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
C VCGD +SG HYG+ SC+ C FFKR+I N Y+C A + C I K R C+A
Sbjct: 6 LCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNE----CEITKRRRKSCQA 61
Query: 100 CRLNKCFMSAMNKD 113
CR K M K+
Sbjct: 62 CRFMKALKVGMLKE 75
>2han_B Ecdysone receptor; transcription regulation, transcription factor,
DNA-binding, nuclear protein, nuclear receptor, zinc
finger; 1.95A {Drosophila melanogaster} SCOP: g.39.1.2
PDB: 1r0o_B 1r0n_B
Length = 119
Score = 103 bits (258), Expect = 3e-30
Identities = 34/82 (41%), Positives = 47/82 (57%), Gaps = 4/82 (4%)
Query: 32 SRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDK 91
S R+ + C VCGDR+SG HY +C+GC GFF+RS+ ++ VY CK C +D
Sbjct: 2 SAPRVQEELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRA----CEMDM 57
Query: 92 THRNQCRACRLNKCFMSAMNKD 113
R +C+ CRL KC M +
Sbjct: 58 YMRRKCQECRLKKCLAVGMRPE 79
>1r4i_A Androgen receptor; AR, steroid receptor, protein-DNA complex,
transcription/DNA complex; 3.10A {Rattus norvegicus}
SCOP: g.39.1.2
Length = 105
Score = 100 bits (251), Expect = 3e-29
Identities = 30/74 (40%), Positives = 40/74 (54%), Gaps = 4/74 (5%)
Query: 40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
C +CGD +SG HYG +C C FFKR+ + Y C ++ D C IDK R C +
Sbjct: 9 TCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRND----CTIDKFRRKNCPS 64
Query: 100 CRLNKCFMSAMNKD 113
CRL KC+ + M
Sbjct: 65 CRLRKCYEAGMTLG 78
>1kb2_A Vitamin D3 receptor; VDR, nuclear receptor, protein-DNA complex,
transcription/DNA complex; 2.70A {Homo sapiens} SCOP:
g.39.1.2 PDB: 1kb4_A 1kb6_A 1ynw_A
Length = 110
Score = 100 bits (250), Expect = 5e-29
Identities = 35/80 (43%), Positives = 49/80 (61%), Gaps = 4/80 (5%)
Query: 34 DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTH 93
DR + C VCGDR++G H+ +C+GC GFF+RS+ R ++TC GD C I K +
Sbjct: 2 DRNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGD----CRITKDN 57
Query: 94 RNQCRACRLNKCFMSAMNKD 113
R C+ACRL +C M K+
Sbjct: 58 RRHCQACRLKRCVDIGMMKE 77
>2nll_B Protein (thyroid hormone receptor); complex (transcription
regulation/DNA), DNA-binding, nuclear protein, zinc-
finger, multigene family; HET: DNA 5IU; 1.90A {Homo
sapiens} SCOP: g.39.1.2 PDB: 3m9e_A*
Length = 103
Score = 96.7 bits (241), Expect = 8e-28
Identities = 36/78 (46%), Positives = 47/78 (60%), Gaps = 6/78 (7%)
Query: 38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRN--RVYTCKAQGDLKGHCPIDKTHRN 95
D C VCGD+++G HY +C+GC GFF+R+I +N Y+CK +G C IDK RN
Sbjct: 1 DELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGK----CVIDKVTRN 56
Query: 96 QCRACRLNKCFMSAMNKD 113
QC+ CR KC M D
Sbjct: 57 QCQECRFKKCIYVGMATD 74
>1lbd_A RXR_LBD, retinoid X receptor; transcription factor, nuclear
receptor, structural proteomic europe, spine, structural
genomics; 2.70A {Homo sapiens} SCOP: a.123.1.1 PDB:
1z5x_U* 2q60_A
Length = 282
Score = 33.2 bits (76), Expect = 0.009
Identities = 1/15 (6%), Positives = 5/15 (33%)
Query: 93 HRNQCRACRLNKCFM 107
H + + + +
Sbjct: 6 HHHHHSSGLVPRGSH 20
>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase
activation, cytochrome C, procaspase-9, A nucleotide,
cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A*
3iyt_A* 3iza_A*
Length = 1249
Score = 31.7 bits (72), Expect = 0.033
Identities = 13/74 (17%), Positives = 25/74 (33%), Gaps = 10/74 (13%)
Query: 23 PDGRDVTSASRD--RLLDIP-CKVCGDRSSGKHYGIYSC----DGC---SGFFKRSIHRN 72
DG + A+++ L DI + + +G H I C + +
Sbjct: 808 ADGDKIIVAAKNKVLLFDIHTSGLLAEIHTGHHSTIQYCDFSPYDHLAVIALSQYCVELW 867
Query: 73 RVYTCKAQGDLKGH 86
+ + D +GH
Sbjct: 868 NIDSRLKVADCRGH 881
>3dm0_A Maltose-binding periplasmic protein fused with RACK1; MBP RACK1A,
receptor for activiated protein C-kinase 1,
beta-propeller WD40 repeat; HET: GLC; 2.40A {Escherichia
coli}
Length = 694
Score = 28.5 bits (64), Expect = 0.46
Identities = 18/83 (21%), Positives = 30/83 (36%), Gaps = 23/83 (27%)
Query: 23 PDGRDVTSASRD---RLLDI---PCKVCGDRSSGKHYGI-----YSCDGC-----SGFFK 66
D R + SASRD +L + + G H +S + S +
Sbjct: 482 LDNRQIVSASRDRTIKLWNTLGECKYTISEGGEG-HRDWVSCVRFSPNTLQPTIVSASWD 540
Query: 67 RSIHRNRV---YTCKAQGDLKGH 86
+++ +V CK + L GH
Sbjct: 541 KTV---KVWNLSNCKLRSTLAGH 560
>2aq5_A Coronin-1A; WD40 repeat, 7-bladed beta-propeller, structural
protein; HET: CME; 1.75A {Mus musculus} PDB: 2b4e_A
Length = 402
Score = 27.7 bits (62), Expect = 0.87
Identities = 13/80 (16%), Positives = 29/80 (36%), Gaps = 12/80 (15%)
Query: 23 PDGRDVTSASRD---RLLDIPCKVCGDRSSGKHYG------IYSCDGC---SGFFKRSIH 70
DG + ++ RD R+++ H G ++ +G +GF + S
Sbjct: 186 RDGALICTSCRDKRVRVIEPRKGTVVAEKDRPHEGTRPVHAVFVSEGKILTTGFSRMSER 245
Query: 71 RNRVYTCKAQGDLKGHCPID 90
+ ++ K + +D
Sbjct: 246 QVALWDTKHLEEPLSLQELD 265
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 27.5 bits (60), Expect = 1.1
Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 7/44 (15%)
Query: 12 PPRYPQYFMSRPDGRDVTSASRDRLLDI-PCK---VCGDRSSGK 51
+ +Y +SR + R LL++ P K + G SGK
Sbjct: 123 NQVFAKYNVSRL--QPYLKL-RQALLELRPAKNVLIDGVLGSGK 163
>2hr0_B Complement C3 alpha' chain; complement component C3B, immune
system; HET: THC; 2.26A {Homo sapiens} PDB: 2icf_B*
2wii_B* 2win_B* 3g6j_B 3l5n_B* 2a73_B* 2i07_B* 2xwj_B*
2xwb_B* 2a74_C* 2ice_C* 2qki_C* 3l3o_F* 3nms_C* 3nsa_C*
3ohx_C* 3t4a_C 2ice_B* 3l3o_B* 3nms_B* ...
Length = 915
Score = 26.6 bits (57), Expect = 2.3
Identities = 8/65 (12%), Positives = 16/65 (24%), Gaps = 2/65 (3%)
Query: 18 YFMSRPDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTC 77
Y + ++ K+C D +C K ++ C
Sbjct: 732 YAYYNLEESCTRFYHPEKEDGKLNKLCRDELCRCAEE--NCFIQKSDDKVTLEERLDKAC 789
Query: 78 KAQGD 82
+ D
Sbjct: 790 EPGVD 794
>3aa0_B F-actin-capping protein subunit beta isoforms 1 A; actin capping
protein, barbed END regulation, carmil family
conformational change; 1.70A {Gallus gallus} PDB:
3aa1_B* 3aa6_B 3aa7_B* 2kxp_B 3lk2_B
Length = 244
Score = 26.4 bits (58), Expect = 2.4
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 11/60 (18%)
Query: 8 CRQIPPRYPQYFMS-----RPDGRDVTSASRDRLLDIPCKVCGDRSSGKHY--GIYSCDG 60
R++PP+ + +S P + +S +D P K+ D+ GK Y Y+ DG
Sbjct: 13 MRRLPPQQIEKNLSDLIDLVPSLCEDLLSS----VDQPLKIARDKVVGKDYLLCDYNRDG 68
>3lk4_B F-actin-capping protein subunit beta isoforms 1 and 2; CAPZ,
CD2AP, actin filaments, uncapping, actin-filament
regulators, protein-protein comple, actin capping,
actin- binding; 1.99A {Gallus gallus} PDB: 2kz7_B
3aaa_B 3aae_B 3lk3_B 1izn_B
Length = 277
Score = 26.4 bits (58), Expect = 2.5
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 11/60 (18%)
Query: 8 CRQIPPRYPQYFMS-----RPDGRDVTSASRDRLLDIPCKVCGDRSSGKHY--GIYSCDG 60
R++PP+ + +S P + +S +D P K+ D+ GK Y Y+ DG
Sbjct: 13 MRRLPPQQIEKNLSDLIDLVPSLCEDLLSS----VDQPLKIARDKVVGKDYLLCDYNRDG 68
>1z5x_E Ecdysone receptor ligand binding domain; ponasterone A, nuclear
receptor, ECR, USP, hormone/growth factor receptor
complex; HET: P1A; 3.07A {Bemisia tabaci}
Length = 310
Score = 26.3 bits (58), Expect = 2.7
Identities = 4/27 (14%), Positives = 7/27 (25%)
Query: 86 HCPIDKTHRNQCRACRLNKCFMSAMNK 112
DK N +C + +
Sbjct: 31 KAQKDKDKPNSTTSCSPDGIKQEIDPQ 57
Score = 25.2 bits (55), Expect = 6.6
Identities = 3/27 (11%), Positives = 10/27 (37%), Gaps = 1/27 (3%)
Query: 87 CPIDKTHRNQCRACRLNKCFMSAMNKD 113
C + K + + + ++ + D
Sbjct: 23 CAV-KRKEKKAQKDKDKPNSTTSCSPD 48
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 25.7 bits (55), Expect = 3.3
Identities = 6/25 (24%), Positives = 10/25 (40%), Gaps = 8/25 (32%)
Query: 66 KRSIHRNRVYTCKAQGDLKGHCPID 90
K+++ K Q LK + D
Sbjct: 19 KQALK-------KLQASLKLYAD-D 35
>4fsd_A Arsenic methyltransferase; rossmann fold; 1.75A {Cyanidioschyzon
SP} PDB: 4fr0_A* 4fs8_A 3p7e_A 3qnh_A 3qhu_A
Length = 383
Score = 25.8 bits (56), Expect = 3.5
Identities = 4/38 (10%), Positives = 10/38 (26%)
Query: 49 SGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGH 86
+H G++ + + L+ H
Sbjct: 342 EQQHMGLFKANDSYALLHAPLSMQVEQLVSGAAALEHH 379
>1wev_A Riken cDNA 1110020M19; structural genomics, PHD domain, riken
structural genomics/proteomics initiative, RSGI, gene
regulation; NMR {Mus musculus} SCOP: g.50.1.2
Length = 88
Score = 24.6 bits (53), Expect = 4.5
Identities = 5/25 (20%), Positives = 9/25 (36%)
Query: 37 LDIPCKVCGDRSSGKHYGIYSCDGC 61
+ + C VC + + C C
Sbjct: 15 MGLACVVCRQMTVASGNQLVECQEC 39
>4akr_B F-actin-capping protein subunit beta; actin-binding protein;
2.20A {Dictyostelium discoideum}
Length = 290
Score = 25.3 bits (55), Expect = 4.6
Identities = 18/65 (27%), Positives = 25/65 (38%), Gaps = 17/65 (26%)
Query: 8 CRQIPPRYPQYFMS-----RPDGRDVTSASRDRLL---DIPCKVCGDRSSGKHY--GIYS 57
R++PP + ++ PD + LL D P KV D S K Y Y+
Sbjct: 31 MRRLPPSQIEDNLAGLLDLVPD-------LTEDLLSSIDQPLKVAYDAVSKKDYLLCDYN 83
Query: 58 CDGCS 62
D S
Sbjct: 84 RDADS 88
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 25.4 bits (55), Expect = 5.1
Identities = 8/47 (17%), Positives = 11/47 (23%), Gaps = 5/47 (10%)
Query: 20 MSRPDGRDVTSASRDRL-LDIPCKVCGDRSSG----KHYGIYSCDGC 61
M+R L + + C C G C C
Sbjct: 2 MTRESIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALC 48
>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin
regulator, metal-binding, finger, signaling protein;
NMR {Homo sapiens}
Length = 71
Score = 24.1 bits (52), Expect = 5.3
Identities = 9/24 (37%), Positives = 10/24 (41%)
Query: 38 DIPCKVCGDRSSGKHYGIYSCDGC 61
D C +C D S I CD C
Sbjct: 16 DAVCSICMDGESQNSNVILFCDMC 39
>2crw_A ARF GAP 3, ADP-ribosylation factor GTPase-activating protein 3;
arfgap domain, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 149
Score = 24.9 bits (54), Expect = 5.5
Identities = 15/59 (25%), Positives = 23/59 (38%), Gaps = 11/59 (18%)
Query: 20 MSRPDGRDVTSASRDRLLDIPCKVCGDRSSGK------HYGIYSCDGCSGFFKRSIHRN 72
M P +D+ + + KVC D + YG++ C CSG HR+
Sbjct: 8 MGDPSKQDILTIFKRLRSVPTNKVCFDCGAKNPSWASITYGVFLCIDCSG-----SHRS 61
>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex,
box H/ACA, snoRNP, pseudouridine synthase, RNA
modification; 1.95A {Methanocaldococcus jannaschii}
SCOP: b.122.1.1 d.265.1.2
Length = 357
Score = 25.4 bits (56), Expect = 5.6
Identities = 5/15 (33%), Positives = 6/15 (40%)
Query: 1 MELFVGNCRQIPPRY 15
+ F G Q PP
Sbjct: 149 FKEFTGRIYQRPPLK 163
>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase,
pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces
cerevisiae} PDB: 3uai_A
Length = 400
Score = 25.1 bits (55), Expect = 5.6
Identities = 5/15 (33%), Positives = 6/15 (40%)
Query: 1 MELFVGNCRQIPPRY 15
+E G Q PP
Sbjct: 143 LENLTGALFQRPPLI 157
>2xzm_R RACK1; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_R
Length = 343
Score = 25.2 bits (56), Expect = 5.6
Identities = 6/13 (46%), Positives = 8/13 (61%)
Query: 23 PDGRDVTSASRDR 35
PD R + SA +R
Sbjct: 128 PDNRQILSAGAER 140
>3frx_A Guanine nucleotide-binding protein subunit beta- like protein;
RACK1, WD40, beta propeller, ribosome, translation,
acetylation; 2.13A {Saccharomyces cerevisiae} PDB:
3izb_a 3o2z_T 3o30_T 3u5c_g 3u5g_g 3rfg_A 3rfh_A 1trj_A
3jyv_R*
Length = 319
Score = 25.2 bits (56), Expect = 5.9
Identities = 4/13 (30%), Positives = 6/13 (46%)
Query: 23 PDGRDVTSASRDR 35
+ S SRD+
Sbjct: 117 KKASMIISGSRDK 129
>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification,
structural genomics, PSI, structure initiative; 1.90A
{Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2
Length = 316
Score = 25.3 bits (56), Expect = 6.1
Identities = 12/41 (29%), Positives = 16/41 (39%), Gaps = 9/41 (21%)
Query: 1 MELFVGNCRQIPPRY--------PQYFMSRPDGRDVTSASR 33
ME G RQ+P Y ++R GR V +R
Sbjct: 107 MERLRGEIRQVPSSVSAIKVGGRRAYRLAR-QGRSVQLEAR 146
>3o47_A ADP-ribosylation factor GTPase-activating protein ribosylation
factor 1; structural genomics consortium, GTPase
activation; HET: GDP; 2.80A {Homo sapiens}
Length = 329
Score = 25.2 bits (55), Expect = 6.1
Identities = 17/55 (30%), Positives = 22/55 (40%), Gaps = 8/55 (14%)
Query: 20 MSRPDGRDVTSASRDRLLDIPCKVCGDRS---SGKHYGIYSCDGCSGFFKRSIHR 71
M+ P R V R + + C CG + YGI+ C CSG HR
Sbjct: 19 MASPRTRKVLKEVRVQDENNVCFECGAFNPQWVSVTYGIWICLECSG-----RHR 68
>3pfq_A PKC-B, PKC-beta, protein kinase C beta type; phosphorylation,
transferase; HET: TPO SEP ANP; 4.00A {Rattus norvegicus}
PDB: 1tbn_A 1tbo_A 2e73_A
Length = 674
Score = 25.4 bits (55), Expect = 6.1
Identities = 10/54 (18%), Positives = 15/54 (27%)
Query: 41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHR 94
C C D G + C CS + H ++C H+
Sbjct: 51 CSHCTDFIWGFGKQGFQCQVCSFVVHKRCHEFVTFSCPGADKGPASDDPRSKHK 104
>1k8k_C P40, ARP2/3 complex 41 kDa subunit, P41-ARC; beta-propeller,
structural protein; 2.00A {Bos taurus} SCOP: b.69.4.1
PDB: 1tyq_C* 1u2v_C* 2p9i_C* 2p9k_C* 2p9l_C 2p9n_C*
2p9p_C* 2p9s_C* 2p9u_C* 3rse_C 3dxm_C* 3dxk_C
Length = 372
Score = 24.9 bits (55), Expect = 6.3
Identities = 8/54 (14%), Positives = 17/54 (31%), Gaps = 12/54 (22%)
Query: 23 PDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYT 76
P+ + S R++ +C + + C K R+ V +
Sbjct: 106 PNEKKFAVGSGSRVI----SIC-YFEQENDWWV-----CKHIKKP--IRSTVLS 147
Score = 24.5 bits (54), Expect = 9.4
Identities = 8/41 (19%), Positives = 15/41 (36%), Gaps = 3/41 (7%)
Query: 23 PDGRDVTSASRD---RLLDIPCKVCGDRSSGKHYGIYSCDG 60
P+ + + S D R+ K +R + +G G
Sbjct: 152 PNSVLLAAGSCDFKCRIFSAYIKEVEERPAPTPWGSKMPFG 192
>3n0a_A Tyrosine-protein phosphatase auxilin; phosphatase-like domain, C2
domain, hydrolase; 2.20A {Bos taurus}
Length = 361
Score = 25.3 bits (54), Expect = 6.4
Identities = 12/107 (11%), Positives = 27/107 (25%)
Query: 1 MELFVGNCRQIPPRYPQYFMSRPDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDG 60
+ R P + D+ + R P + S + +G
Sbjct: 149 AVRLLYAKRPGIGLSPSHRRYLGYMCDLLADKPYRPHFKPLTIKSITVSPVPFFNKQRNG 208
Query: 61 CSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFM 107
C + I ++YT A + + + + +
Sbjct: 209 CRPYCDVLIGETKIYTTCADFERMKEYRVQDGKIFIPLSITVQGDVV 255
>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation,
lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima}
SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A
Length = 309
Score = 24.9 bits (55), Expect = 6.4
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 1 MELFVGNCRQIPPRY 15
+ FVG Q+PP Y
Sbjct: 103 IFSFVGEYDQVPPAY 117
>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop,
lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli}
SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A
Length = 327
Score = 24.9 bits (55), Expect = 7.0
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 1 MELFVGNCRQIPPRY 15
++ F G+ QIP Y
Sbjct: 125 LDTFRGDIEQIPSMY 139
>2hc4_A Vitamin D receptor; alpha helical sandwich, gene regulation; HET:
VDX; 2.20A {Danio rerio} PDB: 2hbh_A* 2hcd_A* 3dr1_A*
3o1d_A* 3o1e_A*
Length = 302
Score = 24.8 bits (54), Expect = 7.4
Identities = 1/20 (5%), Positives = 2/20 (10%)
Query: 93 HRNQCRACRLNKCFMSAMNK 112
+ R
Sbjct: 25 DDSYSDFVRFRPPVREGPVT 44
>4aow_A Guanine nucleotide-binding protein subunit beta-2; receptor,
WD-repeat, beta-propeller; 2.45A {Homo sapiens} PDB:
2zkq_a
Length = 340
Score = 24.8 bits (55), Expect = 7.7
Identities = 6/13 (46%), Positives = 8/13 (61%)
Query: 23 PDGRDVTSASRDR 35
D R + S SRD+
Sbjct: 138 SDNRQIVSGSRDK 150
>3lju_X ARF-GAP with dual PH domain-containing protein 1; structural
genomics consortium, GTPase activation, SGC, binding,
nucleus, phosphoprotein; HET: IP9; 1.70A {Homo sapiens}
PDB: 3feh_A* 3fm8_C 3mdb_C*
Length = 386
Score = 25.1 bits (54), Expect = 7.8
Identities = 9/20 (45%), Positives = 11/20 (55%), Gaps = 5/20 (25%)
Query: 53 YGIYSCDGCSGFFKRSIHRN 72
G++ C CSG IHRN
Sbjct: 52 LGVFICLSCSG-----IHRN 66
>2aus_C Pseudouridine synthase; isomerase, structural protein,
isomerase-structural protein; 2.10A {Pyrococcus abyssi}
PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A*
2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A
Length = 334
Score = 24.5 bits (54), Expect = 9.0
Identities = 6/15 (40%), Positives = 7/15 (46%)
Query: 1 MELFVGNCRQIPPRY 15
M+ F G Q PP
Sbjct: 129 MKEFEGEIIQRPPLR 143
>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from
bromodomain-containing protein...; PHD finger, histone
CODE, transcription; NMR {Homo sapiens}
Length = 88
Score = 23.8 bits (51), Expect = 9.7
Identities = 9/24 (37%), Positives = 10/24 (41%)
Query: 38 DIPCKVCGDRSSGKHYGIYSCDGC 61
D C +C D S I CD C
Sbjct: 25 DAVCSICMDGESQNSNVILFCDMC 48
>3vl1_A 26S proteasome regulatory subunit RPN14; beta-propeller, chaperone,
RPT6; 1.60A {Saccharomyces cerevisiae} PDB: 3acp_A
Length = 420
Score = 24.5 bits (54), Expect = 9.7
Identities = 0/15 (0%), Positives = 4/15 (26%)
Query: 21 SRPDGRDVTSASRDR 35
+ + + +
Sbjct: 299 DGNNANYIYAGYENG 313
>3jue_A Arfgap with coiled-coil, ANK repeat and PH domain containing
protein 1; arfgap domain, zinc-binding module, GTPase
activ metal-binding, nitration; 2.30A {Homo sapiens}
Length = 368
Score = 24.7 bits (53), Expect = 9.8
Identities = 12/60 (20%), Positives = 19/60 (31%), Gaps = 12/60 (20%)
Query: 20 MSRPDGRDVTSASRDRLLDIPC-KVCGDRSSGK------HYGIYSCDGCSGFFKRSIHRN 72
M+R ++ + C D + G+ C CSG IHR+
Sbjct: 23 MARGREPGGVGHVVAQVQSVDGNAQCCDCREPAPEWASINLGVTLCIQCSG-----IHRS 77
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.327 0.141 0.477
Gapped
Lambda K H
0.267 0.0528 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,753,772
Number of extensions: 92779
Number of successful extensions: 589
Number of sequences better than 10.0: 1
Number of HSP's gapped: 568
Number of HSP's successfully gapped: 104
Length of query: 113
Length of database: 6,701,793
Length adjustment: 77
Effective length of query: 36
Effective length of database: 4,551,876
Effective search space: 163867536
Effective search space used: 163867536
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 (21.7 bits)
S2: 51 (23.9 bits)