RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16185
(263 letters)
>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 80
Score = 73.0 bits (179), Expect = 4e-17
Identities = 20/75 (26%), Positives = 30/75 (40%), Gaps = 8/75 (10%)
Query: 6 IISSDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVAC 65
I S C +C +D+ + PC C G+ +VHQACL +WI C
Sbjct: 10 ITPSSQDICRICHCEGDDESP--LITPCHCTGSLHFVHQACLQQWIKSSDT------RCC 61
Query: 66 PQCNTKYFIVYPYRG 80
C ++ + G
Sbjct: 62 ELCKYEFIMETKLSG 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 = 63.2 bits (154), Expect = 1e-13
Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 10/65 (15%)
Query: 8 SSDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQ 67
D+ CW+C ++ + C C G + VH++CL+ W+ + AC
Sbjct: 3 DEDVPVCWICNEELGNE----RFRACGCTGELENVHRSCLSTWLTISRN------TACQI 52
Query: 68 CNTKY 72
C Y
Sbjct: 53 CGVVY 57
>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 = 44.3 bits (104), Expect = 3e-05
Identities = 42/223 (18%), Positives = 71/223 (31%), Gaps = 69/223 (30%)
Query: 67 QCNT-KYF----IVY-PYRGLLVSLLDTIDTAVYKLCPFVAAGVVLGSMY--------WC 112
Q NT YF +Y Y L+ L I + L + + ++ W
Sbjct: 163 QGNTDDYFEELRDLYQTYHVLVGDL---IKFSAETLSELIRTTLDAEKVFTQGLNILEW- 218
Query: 113 AVTYGAVTVMVVSPLHTYLG--ALSLRFCLVHPLVNINRQYRFQLDNILRIC-----DKG 165
+ + T P YL +S PL+ + QL + + G
Sbjct: 219 -LENPSNT-----PDKDYLLSIPISC------PLIGV-----IQLAHYVVTAKLLGFTPG 261
Query: 166 LLR-RLRARQVIGRENGLQVMREVDAIVL----------LLGLPAIPVVLILGWCHIHRH 214
LR L+ G GL V A+ + + AI V+ +G +
Sbjct: 262 ELRSYLKG--ATGHSQGL-----VTAVAIAETDSWESFFVSVRKAITVLFFIGV---RCY 311
Query: 215 QGHPQ-DLPQAA---EVRHAEETTS--VGLRGPATQYVADLVK 251
+ +P LP + + + E S + + + V D V
Sbjct: 312 EAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVN 354
Score = 30.8 bits (69), Expect = 0.59
Identities = 34/206 (16%), Positives = 64/206 (31%), Gaps = 65/206 (31%)
Query: 47 LNRWIDEKQK--GNAFT---QVACP-----QCNTKYFIVYPYRGL----LVSLLDTIDTA 92
+ W++ + ++CP Q Y + G L S L
Sbjct: 215 ILEWLENPSNTPDKDYLLSIPISCPLIGVIQL-AHYVVTAKLLGFTPGELRSYLKGATGH 273
Query: 93 VYKLCPFVAAGVVLGSMYW---CAVTYGAVTVMVVSPLHTYLGALSLRFCLVHPLVNIN- 148
L V A + + W A+TV+ ++G +R +P ++
Sbjct: 274 SQGL---VTAVAIAETDSWESFFVSVRKAITVL------FFIG---VRCYEAYPNTSLPP 321
Query: 149 RQYRFQLDN-------ILRICDKGLLRRLRARQVIGRENGLQVMREVDAIVLLLGLPA-- 199
L+N +L I + L + + + + + N LPA
Sbjct: 322 SILEDSLENNEGVPSPMLSISN---LTQEQVQDYVNKTNS--------------HLPAGK 364
Query: 200 -IPVVLILGWCHIHRH---QGHPQDL 221
+ + L+ G ++ G PQ L
Sbjct: 365 QVEISLVNG----AKNLVVSGPPQSL 386
>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila
melanogaster}
Length = 381
Score = 39.5 bits (91), Expect = 7e-04
Identities = 17/61 (27%), Positives = 21/61 (34%), Gaps = 4/61 (6%)
Query: 14 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVA---CPQCNT 70
C +CFA D + C H CL W G F +V+ CP C
Sbjct: 311 CNICFAYRLDGGEVP-LVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKA 369
Query: 71 K 71
K
Sbjct: 370 K 370
>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 = 0.019
Identities = 13/64 (20%), Positives = 24/64 (37%), Gaps = 7/64 (10%)
Query: 13 YCWVCFAT-HEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAF---TQVACPQC 68
+C +C +DD + +Q C +WVH C N + + + C C
Sbjct: 4 FCPLCDKCYDDDDYESKMMQ---CGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNC 60
Query: 69 NTKY 72
++
Sbjct: 61 TERH 64
>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 = 32.1 bits (73), Expect = 0.050
Identities = 18/88 (20%), Positives = 31/88 (35%), Gaps = 24/88 (27%)
Query: 14 CWVCFATHEDDRNALWVQPCL---CRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNT 70
C +C +A + CL C+ C+ R+++ + CP C+
Sbjct: 18 CVLCG---GYFIDATTIIECLHSFCK--------TCIVRYLETSKY--------CPICDV 58
Query: 71 KYFIVYPYRGLLVSLLDTIDTAVYKLCP 98
+ P + T+ VYKL P
Sbjct: 59 QVHKTRPLLNIRSDK--TLQDIVYKLVP 84
>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin
regulator, metal-binding, finger, signaling protein;
NMR {Homo sapiens}
Length = 71
Score = 29.9 bits (67), Expect = 0.16
Identities = 11/58 (18%), Positives = 17/58 (29%), Gaps = 10/58 (17%)
Query: 14 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTK 71
C +C + N + C + VHQ C + +G C C
Sbjct: 19 CSICMDGESQNSNVI----LFCDMCNLAVHQECYG--VPYIPEGQWL----CRHCLQS 66
>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 = 32.1 bits (72), Expect = 0.20
Identities = 38/272 (13%), Positives = 71/272 (26%), Gaps = 93/272 (34%)
Query: 10 DLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNR-WIDEKQKGNAFTQVACPQC 68
+ Y ++ + R QP + + +R + D Q
Sbjct: 88 RINYKFLMSPIKTEQR-----QPSMMTRM----YIEQRDRLYND-------------NQV 125
Query: 69 NTKYFIVYPYRGLLVSLLDTIDTAVYKLCPFVAAGVVL----GS---------------- 108
KY + R + + A+ +L P A V++ GS
Sbjct: 126 FAKYNV---SR---LQPYLKLRQALLELRP--AKNVLIDGVLGSGKTWVALDVCLSYKVQ 177
Query: 109 ------MYWCAVTYGAVTVMVVSPLHTYLGALSLRFC-LVHPLVNI-------------- 147
++W + V+ L L + + NI
Sbjct: 178 CKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRL 237
Query: 148 --NRQYRFQLDNILR-ICDKGLLRRL----------RARQVIGRENGLQVMREVDAIVLL 194
++ Y L +L + + R +QV + +
Sbjct: 238 LKSKPYENCLL-VLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSA-ATTTHISLDHHS 295
Query: 195 LGL-PAIPVVLILGWCHIHRHQGHPQDLPQAA 225
+ L P L+L + PQDLP+
Sbjct: 296 MTLTPDEVKSLLLKYLDCR-----PQDLPREV 322
>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 = 30.0 bits (67), Expect = 0.22
Identities = 11/58 (18%), Positives = 17/58 (29%), Gaps = 10/58 (17%)
Query: 14 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTK 71
C +C + N + C + VHQ C + +G C C
Sbjct: 28 CSICMDGESQNSNVI----LFCDMCNLAVHQECYG--VPYIPEGQWL----CRHCLQS 75
>3r31_A BADH, betaine aldehyde dehydrogenase; structural genomics,
PSI-biology, NEW YORK structural genomi research
consortium, nysgrc; 2.15A {Agrobacterium tumefaciens}
Length = 517
Score = 31.0 bits (71), Expect = 0.44
Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 5/49 (10%)
Query: 176 IGRENGLQVMR---EVDAIVLLLGLPAIPVVLILGWC--HIHRHQGHPQ 219
GREN + E+ + + G P L + H H H HPQ
Sbjct: 466 FGRENSAAALEHYSELKTVYVSTGKVDAPYAENLYFQSHHHHHHWSHPQ 514
>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 = 29.4 bits (65), Expect = 0.47
Identities = 13/70 (18%), Positives = 20/70 (28%), Gaps = 8/70 (11%)
Query: 3 CLVIISSDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQ 62
C+ ++ Y + + + C S H CL K +
Sbjct: 31 CMEKLAVASGYSDMTDSKALGPMVVGRLTKC-----SHAFHLLCLLAMYCNGNKDGSLQ- 84
Query: 63 VACPQCNTKY 72
CP C T Y
Sbjct: 85 --CPSCKTIY 92
>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 = 29.7 bits (65), Expect = 1.0
Identities = 6/41 (14%), Positives = 11/41 (26%), Gaps = 3/41 (7%)
Query: 8 SSDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLN 48
+ + H + W+ C+ W H C
Sbjct: 37 EKEKPLMSKKKSHHHKKNDFQWIGCDSCQ---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 = 29.0 bits (64), Expect = 1.3
Identities = 10/66 (15%), Positives = 16/66 (24%), Gaps = 8/66 (12%)
Query: 34 LCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCN---TKYFIVYPYRGLLVSLLDTID 90
C +KW C C+ YF +L +
Sbjct: 22 QCGICTKWFTADTFGIDTSSCLPFMTNYSFHCNVCHHSGNTYF-----LRKQANLKEMCL 76
Query: 91 TAVYKL 96
+A+ L
Sbjct: 77 SALANL 82
>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 = 1.4
Identities = 6/29 (20%), Positives = 7/29 (24%), Gaps = 8/29 (27%)
Query: 43 HQACLNRWIDEKQKGNAFTQVACPQCNTK 71
CL + CP C K
Sbjct: 45 CSQCLRDSLKNANT--------CPTCRKK 65
>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 = 3.2
Identities = 6/29 (20%), Positives = 10/29 (34%), Gaps = 6/29 (20%)
Query: 43 HQACLNRWIDEKQKGNAFTQVACPQCNTK 71
H C+ ++ + CP CN
Sbjct: 39 HLPCVAKYFQSNAEPR------CPHCNDY 61
>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 = 26.1 bits (57), Expect = 3.5
Identities = 11/56 (19%), Positives = 22/56 (39%), Gaps = 9/56 (16%)
Query: 13 YCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQC 68
YC +C + + ++ LC+ W H +C+ + + + CP C
Sbjct: 14 YC-LCRQPYNVNH--FMIECGLCQ---DWFHGSCVGIEEENAVDIDIYH---CPDC 60
>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 = 26.0 bits (57), Expect = 3.8
Identities = 6/29 (20%), Positives = 7/29 (24%), Gaps = 8/29 (27%)
Query: 43 HQACLNRWIDEKQKGNAFTQVACPQCNTK 71
CL + CP C K
Sbjct: 40 CSQCLRDSLKNANT--------CPTCRKK 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 = 26.4 bits (57), Expect = 4.3
Identities = 13/60 (21%), Positives = 19/60 (31%), Gaps = 6/60 (10%)
Query: 14 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQAC--LNRWIDEKQKGNAFTQVACPQCNTK 71
C C + DD++A+ KW H+ C + A AC C
Sbjct: 6 CGACRSEVNDDQDAI----LCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKT 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 = 4.4
Identities = 7/36 (19%), Positives = 12/36 (33%), Gaps = 6/36 (16%)
Query: 35 CRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNT 70
C +H C+ ++ + CP CN
Sbjct: 196 CETCGIRMHLPCVAKYFQSNAEPR------CPHCND 225
>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding;
HET: SUC; 1.50A {Homo sapiens}
Length = 64
Score = 25.1 bits (55), Expect = 6.2
Identities = 6/29 (20%), Positives = 7/29 (24%), Gaps = 8/29 (27%)
Query: 43 HQACLNRWIDEKQKGNAFTQVACPQCNTK 71
CL + CP C K
Sbjct: 33 CSQCLRDSLKNANT--------CPTCRKK 53
>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 = 25.2 bits (55), Expect = 7.0
Identities = 13/53 (24%), Positives = 18/53 (33%), Gaps = 20/53 (37%)
Query: 33 CLCRGTS--------------KWVHQACLNRWIDEKQKGNAFTQVACPQCNTK 71
C+C S +W H C+ + E KG + CPQC
Sbjct: 9 CICNQVSYGEMVGCDNQDCPIEWFHYGCVG--LTEAPKGKWY----CPQCTAA 55
>3sy8_A ROCR; TIM barrel phosphodiesterase-A, transcription regulator; HET:
EPE; 2.50A {Pseudomonas aeruginosa}
Length = 400
Score = 26.9 bits (60), Expect = 8.3
Identities = 8/55 (14%), Positives = 19/55 (34%), Gaps = 11/55 (20%)
Query: 152 RFQLDNILRICDKGLLRRLRARQVIGRENG------LQVMREVDAIVLLLGLPAI 200
FQ + L+++ ++ +G L+ VD + L + +
Sbjct: 13 PFQRLVAVT-----ALKKVVPGSILEAADGKEAVAILESCGHVDIAICDLQMSGM 62
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
0.328 0.141 0.464
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: 4,063,682
Number of extensions: 240465
Number of successful extensions: 665
Number of sequences better than 10.0: 1
Number of HSP's gapped: 655
Number of HSP's successfully gapped: 44
Length of query: 263
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 171
Effective length of database: 4,133,061
Effective search space: 706753431
Effective search space used: 706753431
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: 56 (25.8 bits)