RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3895
(185 letters)
>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 80
Score = 69.9 bits (171), Expect = 2e-16
Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 8/69 (11%)
Query: 69 KYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTK 128
C +C +D+ + PC C G+ +VHQACL +WI C C +
Sbjct: 16 DICRICHCEGDDESP--LITPCHCTGSLHFVHQACLQQWIKSSDT------RCCELCKYE 67
Query: 129 YFIVYPYRG 137
+ + G
Sbjct: 68 FIMETKLSG 76
>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace
motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3
Length = 60
Score = 62.4 bits (152), Expect = 6e-14
Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 10/63 (15%)
Query: 67 DLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCN 126
D+ CW+C ++ + C C G + VH++CL+ W+ + AC C
Sbjct: 5 DVPVCWICNEELGNE----RFRACGCTGELENVHRSCLSTWLTISRN------TACQICG 54
Query: 127 TKY 129
Y
Sbjct: 55 VVY 57
>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila
melanogaster}
Length = 381
Score = 39.5 bits (91), Expect = 3e-04
Identities = 18/69 (26%), Positives = 23/69 (33%), Gaps = 4/69 (5%)
Query: 63 ERSVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVA- 121
E + C +CFA D + C H CL W G F +V+
Sbjct: 303 EEDNEELRCNICFAYRLDGGEVP-LVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSF 361
Query: 122 --CPQCNTK 128
CP C K
Sbjct: 362 GQCPFCKAK 370
>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb,
E3-ligase, nuclear protein, chromosomal protein,
transcription regulation; 2.0A {Mus musculus} PDB:
3rpg_B 2h0d_A
Length = 108
Score = 32.9 bits (75), Expect = 0.015
Identities = 18/88 (20%), Positives = 31/88 (35%), Gaps = 24/88 (27%)
Query: 71 CWVCFATHEDDRNALWVQPCL---CRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNT 127
C +C +A + CL C+ C+ R+++ + CP C+
Sbjct: 18 CVLCG---GYFIDATTIIECLHSFCK--------TCIVRYLETSKY--------CPICDV 58
Query: 128 KYFIVYPYRGLLVSLLDTIDTAVYKLCP 155
+ P + T+ VYKL P
Sbjct: 59 QVHKTRPLLNIRSDK--TLQDIVYKLVP 84
>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 = 32.3 bits (72), Expect = 0.049
Identities = 13/64 (20%), Positives = 24/64 (37%), Gaps = 7/64 (10%)
Query: 70 YCWVCFAT-HEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAF---TQVACPQC 125
+C +C +DD + +Q C +WVH C N + + + C C
Sbjct: 4 FCPLCDKCYDDDDYESKMMQ---CGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNC 60
Query: 126 NTKY 129
++
Sbjct: 61 TERH 64
>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator,
metal-binding, finger, signaling protein; NMR {Homo
sapiens}
Length = 71
Score = 29.1 bits (65), Expect = 0.17
Identities = 11/58 (18%), Positives = 17/58 (29%), Gaps = 10/58 (17%)
Query: 71 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTK 128
C +C + N + C + VHQ C + +G C C
Sbjct: 19 CSICMDGESQNSNVI----LFCDMCNLAVHQECYG--VPYIPEGQWL----CRHCLQS 66
>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 = 28.8 bits (64), Expect = 0.29
Identities = 11/58 (18%), Positives = 17/58 (29%), Gaps = 10/58 (17%)
Query: 71 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTK 128
C +C + N + C + VHQ C + +G C C
Sbjct: 28 CSICMDGESQNSNVI----LFCDMCNLAVHQECYG--VPYIPEGQWL----CRHCLQS 75
>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch
signaling, structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus musculus}
SCOP: g.44.1.1
Length = 114
Score = 29.0 bits (64), Expect = 0.40
Identities = 9/30 (30%), Positives = 10/30 (33%), Gaps = 3/30 (10%)
Query: 100 HQACLNRWIDEKQKGNAFTQVACPQCNTKY 129
H CL K + CP C T Y
Sbjct: 66 HLLCLLAMYCNGNKDGSLQ---CPSCKTIY 92
>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 69
Score = 27.2 bits (60), Expect = 0.78
Identities = 6/29 (20%), Positives = 7/29 (24%), Gaps = 8/29 (27%)
Query: 100 HQACLNRWIDEKQKGNAFTQVACPQCNTK 128
CL + CP C K
Sbjct: 45 CSQCLRDSLKNANT--------CPTCRKK 65
>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 = 29.3 bits (64), Expect = 0.89
Identities = 7/80 (8%), Positives = 21/80 (26%), Gaps = 9/80 (11%)
Query: 26 LQHQQDEDQDETSSSVQSPPGVIQSKSDSAGVVVLEIERSVDLKYCWVCFATHEDDRNAL 85
++ + ++ D + + ++ + + H +
Sbjct: 4 MEQKTPKESDRCGGCGKFTHEDDLIALEEEK------KKEKEKPLMSKKKSHHHKKNDFQ 57
Query: 86 WVQPCLCRGTSKWVHQACLN 105
W+ C+ W H C
Sbjct: 58 WIGCDSCQ---TWYHFLCSG 74
>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 = 28.2 bits (62), Expect = 1.1
Identities = 10/66 (15%), Positives = 16/66 (24%), Gaps = 8/66 (12%)
Query: 91 LCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCN---TKYFIVYPYRGLLVSLLDTID 147
C +KW C C+ YF +L +
Sbjct: 22 QCGICTKWFTADTFGIDTSSCLPFMTNYSFHCNVCHHSGNTYF-----LRKQANLKEMCL 76
Query: 148 TAVYKL 153
+A+ L
Sbjct: 77 SALANL 82
>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase,
ubiquitylation, sumoylation, zinc-FI metal binding
protein; 1.80A {Rattus norvegicus}
Length = 71
Score = 26.7 bits (59), Expect = 1.5
Identities = 6/29 (20%), Positives = 7/29 (24%), Gaps = 8/29 (27%)
Query: 100 HQACLNRWIDEKQKGNAFTQVACPQCNTK 128
CL + CP C K
Sbjct: 40 CSQCLRDSLKNANT--------CPTCRKK 60
>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding;
HET: SUC; 1.50A {Homo sapiens}
Length = 64
Score = 26.3 bits (58), Expect = 1.9
Identities = 6/29 (20%), Positives = 7/29 (24%), Gaps = 8/29 (27%)
Query: 100 HQACLNRWIDEKQKGNAFTQVACPQCNTK 128
CL + CP C K
Sbjct: 33 CSQCLRDSLKNANT--------CPTCRKK 53
>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 74
Score = 26.0 bits (57), Expect = 2.1
Identities = 6/29 (20%), Positives = 10/29 (34%), Gaps = 6/29 (20%)
Query: 100 HQACLNRWIDEKQKGNAFTQVACPQCNTK 128
H C+ ++ + CP CN
Sbjct: 39 HLPCVAKYFQSNAEPR------CPHCNDY 61
>3nw0_A Non-structural maintenance of chromosomes element homolog; E3
ligase, Zn, metal binding protein; 2.92A {Homo sapiens}
Length = 238
Score = 27.4 bits (60), Expect = 2.8
Identities = 7/36 (19%), Positives = 12/36 (33%), Gaps = 6/36 (16%)
Query: 92 CRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNT 127
C +H C+ ++ + CP CN
Sbjct: 196 CETCGIRMHLPCVAKYFQSNAEPR------CPHCND 225
>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 = 25.7 bits (56), Expect = 3.6
Identities = 11/56 (19%), Positives = 22/56 (39%), Gaps = 9/56 (16%)
Query: 70 YCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQC 125
YC +C + + ++ LC+ W H +C+ + + + CP C
Sbjct: 14 YC-LCRQPYNVNH--FMIECGLCQ---DWFHGSCVGIEEENAVDIDIYH---CPDC 60
>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 = 26.0 bits (56), Expect = 4.7
Identities = 13/60 (21%), Positives = 19/60 (31%), Gaps = 6/60 (10%)
Query: 71 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQAC--LNRWIDEKQKGNAFTQVACPQCNTK 128
C C + DD++A+ KW H+ C + A AC C
Sbjct: 6 CGACRSEVNDDQDAI----LCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKT 61
>2nru_A Interleukin-1 receptor-associated kinase 4; inhibitor, IRAK,
transferase; HET: TPO SEP T12; 2.00A {Homo sapiens} PDB:
2nry_A* 2oib_A* 2oic_A* 2oid_A* 2o8y_A*
Length = 307
Score = 26.4 bits (59), Expect = 6.2
Identities = 14/47 (29%), Positives = 19/47 (40%), Gaps = 15/47 (31%)
Query: 51 KSD--SAGVVVLEI---ERSVDLKYCWVCFATHEDDRNAL-WVQPCL 91
KSD S GVV+LEI +VD H + + L +
Sbjct: 214 KSDIYSFGVVLLEIITGLPAVD---------EHREPQLLLDIKEEIE 251
>1x4i_A Inhibitor of growth protein 3; structural genomics, PHD domain,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 70
Score = 24.8 bits (54), Expect = 7.1
Identities = 13/53 (24%), Positives = 18/53 (33%), Gaps = 20/53 (37%)
Query: 90 CLCRGTS--------------KWVHQACLNRWIDEKQKGNAFTQVACPQCNTK 128
C+C S +W H C+ + E KG + CPQC
Sbjct: 9 CICNQVSYGEMVGCDNQDCPIEWFHYGCVG--LTEAPKGKWY----CPQCTAA 55
>1nlf_A Regulatory protein REPA; replicative DNA helicase structural
changes, replication; 1.95A {Escherichia coli} SCOP:
c.37.1.11 PDB: 1g8y_A 1olo_A
Length = 279
Score = 25.8 bits (56), Expect = 8.6
Identities = 8/25 (32%), Positives = 10/25 (40%)
Query: 158 AAGVVLGSMYWCAVTYGAVTVMVHH 182
V+G M A G V +HH
Sbjct: 155 PMAQVIGRMEAIAADTGCSIVFLHH 179
>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD
domain, histone-lysine N-methyltransferase, H3 lysine-4
specific MLL3; NMR {Homo sapiens}
Length = 111
Score = 24.9 bits (54), Expect = 9.1
Identities = 12/59 (20%), Positives = 17/59 (28%), Gaps = 10/59 (16%)
Query: 67 DLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQC 125
+ K C C + ED + +C K H CL + C C
Sbjct: 53 ECKVCQNCKQSGEDSKM------LVCDTCDKGYHTFCLQPVMKSVPTNGWK----CKNC 101
>1kqn_A Nmnat, nicotinamide mononucleotide adenylyl transferase;
nucleotidyltransferase superfamily; HET: NAD; 2.20A
{Homo sapiens} SCOP: c.26.1.3 PDB: 1kqo_A* 1kr2_A*
1kku_A 1gzu_A*
Length = 279
Score = 25.8 bits (56), Expect = 9.4
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 3/53 (5%)
Query: 3 RQRERNERS---LVNEAVLMAIQRHGLQHQQDEDQDETSSSVQSPPGVIQSKS 52
R+ R +S LV + V I++H L + ED++ ++K+
Sbjct: 227 RRALRRGQSIRYLVPDLVQEYIEKHNLYSSESEDRNAGVILAPLQRNTAEAKT 279
>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 = 9.8
Identities = 12/58 (20%), Positives = 19/58 (32%), Gaps = 17/58 (29%)
Query: 109 DEKQKGNAFTQVACPQCNT-KYFIVYPY-RGLLVSLLDTIDTAVYKLCPFVAAGVVLG 164
++ N + CP+C IV + G D + C G+VL
Sbjct: 11 AGRRGPNLNIVLTCPECKVYPPKIVERFSEG------DVV-------CA--LCGLVLS 53
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
0.322 0.133 0.429
Gapped
Lambda K H
0.267 0.0544 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,714,446
Number of extensions: 142399
Number of successful extensions: 315
Number of sequences better than 10.0: 1
Number of HSP's gapped: 310
Number of HSP's successfully gapped: 41
Length of query: 185
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 97
Effective length of database: 4,244,745
Effective search space: 411740265
Effective search space used: 411740265
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 (22.0 bits)
S2: 54 (25.0 bits)