RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16699
(231 letters)
>1wep_A PHF8; structural genomics, PHD domain, riken structural
genomics/proteomics initiative, RSGI, DNA binding
protein; NMR {Mus musculus} SCOP: g.50.1.2
Length = 79
Score = 40.3 bits (94), Expect = 3e-05
Identities = 18/65 (27%), Positives = 27/65 (41%), Gaps = 7/65 (10%)
Query: 110 NNTYNQNFKGKYCTCARPYPDEENPNCDEMIQCALCEDWFHSGHLGLDSPIPDGEDYSEM 169
+ + YC C +PY MI+C LC+DWFH +G++ + D
Sbjct: 3 SGSSGMALVPVYCLCRQPYNVNH-----FMIECGLCQDWFHGSCVGIEE--ENAVDIDIY 55
Query: 170 SCASC 174
C C
Sbjct: 56 HCPDC 60
>3kv5_D JMJC domain-containing histone demethylation protein 1D;
epigenetics, histone CODE, jumonji lysine demethylase,
metal-binding, zinc, zinc-finger; HET: OGA; 2.39A {Homo
sapiens} PDB: 3kv6_A*
Length = 488
Score = 40.4 bits (93), Expect = 3e-04
Identities = 24/111 (21%), Positives = 40/111 (36%), Gaps = 6/111 (5%)
Query: 121 YCTCARPYPDEENPNCDEMIQCALCEDWFHSGHLGLDSPIPDG-EDYSEMSCASCINMYP 179
YC C +PY D MI+C +C+DWFH +G++ + Y +CA
Sbjct: 39 YCVCRQPY-DVNRF----MIECDICKDWFHGSCVGVEEHHAVDIDLYHCPNCAVLHGSSL 93
Query: 180 VLKLYPHLLECPIKDKDVSSIPPVTEAFFWQEGWRSQLCSCEKCLDQQIPD 230
+ K + D S F +E S ++ + +
Sbjct: 94 MKKRRNWHRHDYTEIDDGSKPVQAGTRTFIKELRSRVFPSADEIIIKMHGS 144
>3kv4_A PHD finger protein 8; epigenetics, histone CODE, covalent histone
modifications, jumonji demethylase, mental retardation,
metal-binding, zinc; HET: M3L MLY OGA; 2.19A {Homo
sapiens}
Length = 447
Score = 39.2 bits (90), Expect = 8e-04
Identities = 21/111 (18%), Positives = 35/111 (31%), Gaps = 8/111 (7%)
Query: 121 YCTCARPYPDEENPNCDEMIQCALCEDWFHSGHLGLDSPIPDGEDYSEMSCASCINMYPV 180
YC C PY MI+C +C+DWFH +G+ D C +C ++
Sbjct: 7 YCLCRLPYDVTR-----FMIECDMCQDWFHGSCVGV--EEEKAADIDLYHCPNCEVLHGP 59
Query: 181 LKLYPHLLECPIKDKDVSSIPPVTEAFFWQEGWRSQLCSCEKCLDQQIPDL 231
+ P T + + RS+ + +
Sbjct: 60 SIMKKR-RGSSKGHDTHKGKPVKTGSPTFVRELRSRTFDSSDEVILKPTGN 109
>3pur_A Lysine-specific demethylase 7 homolog;
oxidoreductase-oxidoreductase inhibitor complex; HET:
2HG; 2.10A {Caenorhabditis elegans} PDB: 3n9l_A 3n9m_A*
3n9o_A* 3n9p_A* 3n9q_A* 3n9n_A* 3puq_A*
Length = 528
Score = 37.0 bits (84), Expect = 0.004
Identities = 6/30 (20%), Positives = 12/30 (40%), Gaps = 2/30 (6%)
Query: 121 YCTCARPYPDEENPNCDEMIQCALCEDWFH 150
+ + + N + I C C+ W+H
Sbjct: 42 LMSKKKSHH--HKKNDFQWIGCDSCQTWYH 69
>1wem_A Death associated transcription factor 1; structural genomics, PHD
domain, death inducer- obliterator 1(DIO-1); NMR {Mus
musculus} SCOP: g.50.1.2
Length = 76
Score = 34.1 bits (78), Expect = 0.004
Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 8/56 (14%)
Query: 121 YCTCARPYPDEENPNCDEMIQCALCEDWFHSGHLGLDSPIPDGEDYSEMS--CASC 174
YC C +P+ + MI C CE+WFH +G+ + + C +C
Sbjct: 18 YCICRQPHNNRF------MICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNC 67
>3kqi_A GRC5, PHD finger protein 2; metal-binding, zinc-finger,
histone-binding, NUC protein; HET: M3L; 1.78A {Homo
sapiens}
Length = 75
Score = 34.1 bits (78), Expect = 0.004
Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 7/63 (11%)
Query: 121 YCTCARPYPDEENPNCDEMIQCALCEDWFHSGHLGLDSPIPDGEDYSEMSCASCINMYPV 180
YC C PY MI+C C+DWFH +G++ + D C +C +
Sbjct: 12 YCVCRLPYDVTR-----FMIECDACKDWFHGSCVGVEE--EEAPDIDIYHCPNCEKTHGK 64
Query: 181 LKL 183
L
Sbjct: 65 STL 67
>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain,
leukemia, apoptosis, chromati regulator, DNA-binding,
isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A*
3lqj_A* 2kyu_A
Length = 183
Score = 34.2 bits (77), Expect = 0.017
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 119 GKYCT-CARPYPDEENPNCDEMIQCALCEDWFHS 151
G +C C + Y D++ +M+QC C+ W HS
Sbjct: 2 GNFCPLCDKCYDDDDYE--SKMMQCGKCDRWVHS 33
>3o7a_A PHD finger protein 13 variant; PHF13, zinc finger, PHD domain,
nuclear protein, structural structural genomics
consortium, SGC, protein binding; HET: M3L; 1.67A {Homo
sapiens}
Length = 52
Score = 30.8 bits (70), Expect = 0.043
Identities = 9/30 (30%), Positives = 12/30 (40%), Gaps = 6/30 (20%)
Query: 121 YCTCARPYPDEENPNCDEMIQCALCEDWFH 150
C C +P+ MI+C C W H
Sbjct: 6 TCFCMKPFAGRP------MIECNECHTWIH 29
>1wee_A PHD finger family protein; structural genomics, PHD domain, riken
structural genomics/proteomics initiative, RSGI, DNA
binding protein; NMR {Arabidopsis thaliana} SCOP:
g.50.1.2
Length = 72
Score = 31.4 bits (71), Expect = 0.044
Identities = 12/54 (22%), Positives = 19/54 (35%), Gaps = 8/54 (14%)
Query: 121 YCTCARPYPDEENPNCDEMIQCALCEDWFHSGHLGLDSPIPDGEDYSEMSCASC 174
C C D E M+ C C W H+ +G+++ + C C
Sbjct: 18 DCKCGTKDDDGE-----RMLACDGCGVWHHTRCIGINNADALPSKF---LCFRC 63
>3o70_A PHD finger protein 13; PHF13, structural genomics consortium, SGC,
structural genom type zinc finger, protein binding, zinc
ION binding; 1.85A {Homo sapiens}
Length = 68
Score = 30.6 bits (69), Expect = 0.061
Identities = 9/30 (30%), Positives = 12/30 (40%), Gaps = 6/30 (20%)
Query: 121 YCTCARPYPDEENPNCDEMIQCALCEDWFH 150
C C +P+ MI+C C W H
Sbjct: 21 TCFCMKPFAGRP------MIECNECHTWIH 44
>2kgg_A Histone demethylase jarid1A; PHD finger, histone modification,
leukemia, alternative splicing, chromatin regulator,
developmental protein; NMR {Homo sapiens} PDB: 2kgi_A*
3gl6_A*
Length = 52
Score = 29.9 bits (67), Expect = 0.077
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 6/52 (11%)
Query: 122 CTCARPYPDEENPNCDEMIQC-ALCEDWFHSGHLGLDSPIPDGEDYSEMSCA 172
C RP D+ + +QC C++WFH +G+ + + EDY ++CA
Sbjct: 6 QNCQRPCKDKVD-----WVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA 52
>1we9_A PHD finger family protein; structural genomics, PHD domain, riken
structural genomics/proteomics initiative, RSGI, DNA
binding protein; NMR {Arabidopsis thaliana} SCOP:
g.50.1.2
Length = 64
Score = 29.4 bits (66), Expect = 0.19
Identities = 17/60 (28%), Positives = 21/60 (35%), Gaps = 8/60 (13%)
Query: 118 KGKYCT-CARPYPDEENPNCDEMIQCALCEDWFHSGHLGLDSPIPDGEDYSEMSCASCIN 176
C C Y +E I C LCE WFH + + E + C SC N
Sbjct: 5 SSGQCGACGESYAADEF-----WICCDLCEMWFHGKCVKITP--ARAEHIKQYKCPSCSN 57
>2ri7_A Nucleosome-remodeling factor subunit BPTF; zinc finger,
alpha-helical bundle, dimethyl-lysine, bromodom
chromatin regulator, metal-binding, nucleus; HET: MLY;
1.45A {Homo sapiens} PDB: 2fsa_A* 2f6n_A 2f6j_A* 3qzv_A*
3uv2_A* 3qzt_A* 3qzs_A* 2fui_A 2fuu_A*
Length = 174
Score = 30.6 bits (69), Expect = 0.25
Identities = 11/70 (15%), Positives = 21/70 (30%), Gaps = 5/70 (7%)
Query: 121 YCTCARPYPDEENPNCDEMIQCALCEDWFHSGHLGLDSPIPDGEDYSEMSCASCINMYPV 180
YC C P + + I C C++W+H +G+ + D
Sbjct: 10 YCICKTPEDESKF-----YIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAMT 64
Query: 181 LKLYPHLLEC 190
+ +
Sbjct: 65 VLTPLTEKDY 74
>3ny3_A E3 ubiquitin-protein ligase UBR2; zinc finger-like, ubiquitin
ligase, protein binding, lygase,; 1.60A {Homo sapiens}
PDB: 3ny2_A 3ny1_A
Length = 75
Score = 29.1 bits (65), Expect = 0.27
Identities = 12/60 (20%), Positives = 20/60 (33%), Gaps = 6/60 (10%)
Query: 44 KRQALYACLTCTPDICDPAGFCLAC-NYHCHEGHN---IVELYTKRCDCGNSKFGEKKCN 99
+ Y+C C D C+ C H H CDCG+++ ++
Sbjct: 13 VGEPTYSCRDCAVD--PTCVLCMECFLGSIHRDHRYRMTTSGGGGFCDCGDTEAWKEGPY 70
>2k16_A Transcription initiation factor TFIID subunit 3; protein,
alternative splicing, metal-binding, nucleus,
phosphoprotein, transcription regulation; NMR {Mus
musculus} PDB: 2k17_A*
Length = 75
Score = 28.7 bits (64), Expect = 0.44
Identities = 11/46 (23%), Positives = 19/46 (41%), Gaps = 6/46 (13%)
Query: 121 YCTCARPYPDEENPNCDEMIQCALCEDWFHSGHLGLDSPIPDGEDY 166
C +P MI C C+DW+H +G+ + P+ +
Sbjct: 21 CPGCNKPDDGSP------MIGCDDCDDWYHWPCVGIMAAPPEEMQW 60
>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 = 30.2 bits (67), Expect = 0.58
Identities = 36/221 (16%), Positives = 64/221 (28%), Gaps = 57/221 (25%)
Query: 42 YMKRQALYACLTCTPDICDP---AGFCLACNYHCHEGHNIVELYTKRCDCGNSKF----G 94
+K + CL ++ + F N C I L T R + F
Sbjct: 237 LLKSKPYENCLLVLLNVQNAKAWNAF----NLSC----KI--LLTTR-FKQVTDFLSAAT 285
Query: 95 EKKCNLEPNKDALNVNNTYNQNFKGKYCTC-ARPYPDEE---NPNCDEMIQCALCED--- 147
+L+ + L + ++ KY C + P E NP +I D
Sbjct: 286 TTHISLDHHSMTLTPDEV--KSLLLKYLDCRPQDLPREVLTTNPRRLSIIA-ESIRDGLA 342
Query: 148 ----WFHSGHLGLDSPIPDGEDYSEMSCASCINMYPVLKLYPHLLECPIKDKDVSSIPPV 203
W H L + I S +N+ + + IP +
Sbjct: 343 TWDNWKHVNCDKLTTII-----------ESSLNVLEPAEYRKMFDRLSVFPPSAH-IPTI 390
Query: 204 TEAFFWQEGWRSQ----LCSCEK--CLDQQ-------IPDL 231
+ W + +S + K +++Q IP +
Sbjct: 391 LLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI 431
>2xb1_A Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro; fusion protein,
signal transduction, transcription, metal BI WNT
proteins; 1.90A {Homo sapiens}
Length = 105
Score = 28.3 bits (62), Expect = 0.81
Identities = 13/69 (18%), Positives = 21/69 (30%), Gaps = 9/69 (13%)
Query: 122 CTCARPYPDEENPNCDEMIQC-ALCEDWFHSGHLGLDSP---IPDGEDYSEMSCASCINM 177
C D+ + I C A C+ WFH G+ + E + +C C+
Sbjct: 7 GACRSEVNDD-----QDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKT 61
Query: 178 YPVLKLYPH 186
Sbjct: 62 KEGSGSGSG 70
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 29.2 bits (65), Expect = 1.5
Identities = 39/256 (15%), Positives = 62/256 (24%), Gaps = 115/256 (44%)
Query: 18 DHLEESAVAVLGAADDKNCT-YS----QG----YMKR-QALYACLTCTP---DICDPAGF 64
D SA+ A + N + QG Y + + LY T D+ +
Sbjct: 138 DKKSNSAL--FRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQ--TYHVLVGDLIKFSAE 193
Query: 65 CLA--------CNYHCHEGHNIVELYTKRCDCGNSKFGEKKCNLEPNKDALNVNNTYNQN 116
L+ +G NI+E + P+KD L
Sbjct: 194 TLSELIRTTLDAEKVFTQGLNILEWLENP-------------SNTPDKDYL--------- 231
Query: 117 FKGKYCTCARPYPDEENPNCDEMI---QCA----LCEDWFHSGHLGLDSPIPDGEDYSEM 169
+ P +I Q A + LG +P GE S +
Sbjct: 232 -----LSIPISCP---------LIGVIQLAHYVVTAK------LLGF-TP---GELRSYL 267
Query: 170 SC----------ASCI-------NMYPVLKLYPHLLECPIKDKDVSSIPPVTEAFFWQEG 212
A I + + ++ +L F+ G
Sbjct: 268 KGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVL-------------------FFI-G 307
Query: 213 WRSQLCSCEKCLDQQI 228
R L I
Sbjct: 308 VRCYEAYPNTSLPPSI 323
>3nis_A E3 ubiquitin-protein ligase UBR1; E3 ubiquitin ligase, UBR BOX,
zinc-binding protein, N-END RU ligase, metal binding
protein; 1.68A {Saccharomyces cerevisiae} PDB: 3nii_A
3nij_A 3nih_A 3nik_A 3nim_A 3nin_A 3nil_A 3nit_A
Length = 82
Score = 26.5 bits (58), Expect = 2.4
Identities = 15/62 (24%), Positives = 22/62 (35%), Gaps = 8/62 (12%)
Query: 44 KRQALYACLTCTPDICDPAGFCLAC-NYHCHEGHNIVELYTKR-----CDCGNSKFGEKK 97
+ LY C C D D C+ C N H H++ CDCG+ +
Sbjct: 17 IGEPLYRCHECGCD--DTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEAWNSP 74
Query: 98 CN 99
+
Sbjct: 75 LH 76
>3rsn_A SET1/ASH2 histone methyltransferase complex subun; PHD domain,
winged helix domain, binding, transcription; 2.10A {Homo
sapiens} PDB: 3s32_A
Length = 177
Score = 27.8 bits (61), Expect = 2.5
Identities = 9/60 (15%), Positives = 16/60 (26%), Gaps = 6/60 (10%)
Query: 116 NFKGKYCTCARPYPDEENPNCDEMIQCALCEDWFHSGHLG-LDSPIPDGEDYSEMSCASC 174
+ + + + +QC +C WF + G S C C
Sbjct: 2 DTQAGSVDE-----ENGRQLGEVELQCGICTKWFTADTFGIDTSSCLPFMTNYSFHCNVC 56
>1z05_A Transcriptional regulator, ROK family; structural genomics, protein
structure initiative, midwest center for structural
genomics; 2.00A {Vibrio cholerae o1 biovar eltor} SCOP:
a.4.5.63 c.55.1.10 c.55.1.10
Length = 429
Score = 27.7 bits (62), Expect = 3.1
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 75 GHNIVELYTKRCDCGN 90
GH ++ KRC CGN
Sbjct: 268 GHIQIDPQGKRCHCGN 283
>1z6r_A MLC protein; transcriptional repressor, ROK family protein, DNA
binding P helix-turn-helix, phosphotransferase system;
2.70A {Escherichia coli} SCOP: a.4.5.63 c.55.1.10
c.55.1.10 PDB: 3bp8_A
Length = 406
Score = 27.3 bits (61), Expect = 4.4
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 75 GHNIVELYTKRCDCGN 90
GH V+ Y KRC CGN
Sbjct: 246 GHTQVDPYGKRCYCGN 261
>2gqw_A Ferredoxin reductase; flavoprotein, oxidoreductase; HET: FAD; 1.40A
{Pseudomonas SP} PDB: 1f3p_A* 1d7y_A* 2gr0_A* 2gr1_A*
2gr2_A* 2yvf_A* 2yvg_A* 2yvj_A* 2gr3_A*
Length = 408
Score = 27.2 bits (61), Expect = 4.8
Identities = 6/23 (26%), Positives = 11/23 (47%), Gaps = 1/23 (4%)
Query: 9 TLGDVLALQDHLEESA-VAVLGA 30
TL D +Q L + + ++G
Sbjct: 131 TLEDARRIQAGLRPQSRLLIVGG 153
>3htv_A D-allose kinase, allokinase; NP_418508.1, structural genomics,
joint CEN structural genomics, JCSG, protein structure
initiative; HET: MSE; 1.95A {Escherichia coli k-12}
Length = 310
Score = 26.8 bits (60), Expect = 5.5
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 75 GHNIVELYTKRCDCGN 90
GH + T+ C CGN
Sbjct: 166 GHIPLGDMTQHCACGN 181
>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway,
WNT signaling complex, chromosomal rearrangement,
signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A
2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A*
Length = 65
Score = 24.7 bits (53), Expect = 7.8
Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 9/58 (15%)
Query: 122 CTCARPYPDEENPNCDEMIQC-ALCEDWFHSGHLGLDSP---IPDGEDYSEMSCASCI 175
C D+ + I C A C+ WFH G+ + E + C +C+
Sbjct: 12 GICTNEVNDD-----QDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTCM 64
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
0.320 0.137 0.460
Gapped
Lambda K H
0.267 0.0531 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,675,828
Number of extensions: 214342
Number of successful extensions: 802
Number of sequences better than 10.0: 1
Number of HSP's gapped: 771
Number of HSP's successfully gapped: 115
Length of query: 231
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 141
Effective length of database: 4,188,903
Effective search space: 590635323
Effective search space used: 590635323
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: 56 (25.8 bits)