RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3674
(306 letters)
>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 80
Score = 86.9 bits (215), Expect = 5e-22
Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 3/70 (4%)
Query: 81 GSEHDENAPVCRICHG---SHENLKALCECRGTMGLVHAECLTQWLSESGRSCCEICNFK 137
S + +CRICH L C C G++ VH CL QW+ S CCE+C ++
Sbjct: 8 TSITPSSQDICRICHCEGDDESPLITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYE 67
Query: 138 YKFKRTLKRP 147
+ + L P
Sbjct: 68 FIMETKLSGP 77
>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 = 81.3 bits (201), Expect = 4e-20
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 85 DENAPVCRICH-GSHENLKALCECRGTMGLVHAECLTQWLSESGRSCCEICNFKYKFK 141
DE+ PVC IC+ C C G + VH CL+ WL+ S + C+IC Y +
Sbjct: 3 DEDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNTR 60
>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 = 39.1 bits (91), Expect = 1e-04
Identities = 11/54 (20%), Positives = 20/54 (37%), Gaps = 3/54 (5%)
Query: 82 SEHDENAPVCRICHGSHENLKALCECRGTMGLVHAECLTQWLSESGRSCCEICN 135
+ + +C ICH ++ C M H C+ ++ + C CN
Sbjct: 9 ETYPDAVKICNICHSLLIQGQSCETCGIRM---HLPCVAKYFQSNAEPRCPHCN 59
>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 = 39.1 bits (90), Expect = 0.001
Identities = 50/365 (13%), Positives = 118/365 (32%), Gaps = 113/365 (30%)
Query: 2 VRKEFSFISKTTRHIETVVNGMDDDKNKLVNRKEHKKSSSASIVSDLDAEEHSQQDDADF 61
+ ++ S + +I+ ++ + + +L+ K ++ +V L ++++ +A
Sbjct: 209 IDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC---LLV--LLNVQNAKAWNA-- 261
Query: 62 FNSICNDILQLL-----EGEIDEIGSEHDENAPVCRICHG-SHENLKALCECRGTMGLVH 115
FN C ++L + D + + + + + + +K+L
Sbjct: 262 FNLSC----KILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL---------- 307
Query: 116 AECLTQWLSESGRSCCE-----ICNFKYKFKRTLKRPLWETMAGWLY-------KVVENS 163
+ L + R + + L W+ W + ++E+S
Sbjct: 308 LKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLAT--WDN---WKHVNCDKLTTIIESS 362
Query: 164 ----------QVFIILSWLMA---ITPIVLLAAALTNNFPFNHNDRKTHQQLQCGFDVRY 210
++F LS I I+L + + + + + +L +Y
Sbjct: 363 LNVLEPAEYRKMFDRLSVFPPSAHIPTILL--SLIWFDVIKS-DVMVVVNKL-----HKY 414
Query: 211 AMIRKDSCP--ISITPIY------------------EGYAMIRKDSCPISITPIYEGKYF 250
+++ K ISI IY + Y + + + P Y +YF
Sbjct: 415 SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKT-FDSDDLIPPYLDQYF 473
Query: 251 KN-----MRTQVLSQLV-----WYYDMLFMI--VRAYFENWH-------------FY--Y 283
+ ++ + + + D F+ +R W+ FY Y
Sbjct: 474 YSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPY 533
Query: 284 IRDHD 288
I D+D
Sbjct: 534 ICDND 538
Score = 34.8 bits (79), Expect = 0.040
Identities = 18/85 (21%), Positives = 32/85 (37%), Gaps = 9/85 (10%)
Query: 6 FSFISKTTRHIETVVNGMDDDKNKLVNRKEHKK------SSSASIVSDLDAEEHSQQDDA 59
F F+ + RH T N N L K +K +V+ + + + +
Sbjct: 500 FRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAI--LDFLPKIEE 557
Query: 60 DFFNSICNDILQL-LEGEIDEIGSE 83
+ S D+L++ L E + I E
Sbjct: 558 NLICSKYTDLLRIALMAEDEAIFEE 582
>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 = 38.9 bits (90), Expect = 0.002
Identities = 26/177 (14%), Positives = 48/177 (27%), Gaps = 52/177 (29%)
Query: 114 VHAECLTQWLSESGRSCC----EICNFKYKFKRTLKRPLWETMAGWLYKVVENSQ----- 164
+HA L L + + E+ + KRP + L++ V
Sbjct: 101 IHA--LAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVA 158
Query: 165 VF----IILSWL-----------MAITPIVLLAAALTNNFPFNHND-RKTHQQLQCGFDV 208
+F + + + ++ +A + D K Q G ++
Sbjct: 159 IFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQ---GLNI 215
Query: 209 RYAMIRKDSCPISITPIYEGYAMIRKDSCPISITPIYEGKYFKNMRTQVLSQLVWYY 265
+ + P + Y S PIS I + QL Y
Sbjct: 216 LEWLENPSNTP------DKDYL----LSIPISCPLI------------GVIQLAHYV 250
Score = 36.6 bits (84), Expect = 0.012
Identities = 26/143 (18%), Positives = 51/143 (35%), Gaps = 31/143 (21%)
Query: 138 YKFKRTLKRPLWETMAGWLYKVVEN--------SQVFIILSWLM--AITP--IVLLAAAL 185
Y+ L L + A L +++ +Q IL WL + TP LL+ +
Sbjct: 177 YQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPI 236
Query: 186 TNNFPFNHNDRKTHQQLQCGFDVRYAMIRK--DSCPISITPIYEGYAMIRKD---SCPIS 240
+ P +Q Y + K P + +G + + I+
Sbjct: 237 S--CPLI-------GVIQL---AHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIA 284
Query: 241 ITPIYEGKYFKNMRTQVLSQLVW 263
T +E +F ++R + ++ L +
Sbjct: 285 ETDSWES-FFVSVR-KAITVLFF 305
Score = 31.6 bits (71), Expect = 0.39
Identities = 15/121 (12%), Positives = 34/121 (28%), Gaps = 45/121 (37%)
Query: 198 THQQLQCGFDV-----RYAMIRKDSCPISITPIYEGYAMIRKDSCPISITPIYEGKY--F 250
+H L+ V A ++ + EG+A D P + + GK+ +
Sbjct: 12 SHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFA---ADDEPTTPAELV-GKFLGY 67
Query: 251 ---------KNMRTQVLSQLVWYYDMLFM-------------------------IVRAYF 276
QVL+ + ++ ++ +++ Y
Sbjct: 68 VSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYI 127
Query: 277 E 277
Sbjct: 128 T 128
Score = 30.8 bits (69), Expect = 0.77
Identities = 22/124 (17%), Positives = 35/124 (28%), Gaps = 45/124 (36%)
Query: 41 SASIVSDLDAEEHSQQDD----------------ADFFNSICNDILQLLE--GEIDEIGS 82
+ DL ++ D AD SI +++++ G ++
Sbjct: 1740 EKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVM-SI-ESLVEVVFYRGMTMQVAV 1797
Query: 83 EHDENA----------PVCRICHGSHENLKALCECRGTMGLVHAECLTQWLSESGRSCCE 132
DE P S E L+ + E V T WL E
Sbjct: 1798 PRDELGRSNYGMIAINPGRVAASFSQEALQYVVER------VGKR--TGWL-------VE 1842
Query: 133 ICNF 136
I N+
Sbjct: 1843 IVNY 1846
Score = 29.6 bits (66), Expect = 1.7
Identities = 27/180 (15%), Positives = 48/180 (26%), Gaps = 52/180 (28%)
Query: 30 LVNRKEHKKSSSASIVSDLDAEEHSQQDDADFFNSICNDILQLLEGEI----DEIGSEHD 85
+ R KKS+SA + +A +I Q G +E+ +
Sbjct: 132 MAKRPFDKKSNSALF-------RAVGEGNAQLV-AIFGG--Q---GNTDDYFEELRDLYQ 178
Query: 86 ENAP-VCRICHGSHENLKALCECRGTMGLVHAECL--TQWLSESGR------------SC 130
V + S E L L V + L +WL SC
Sbjct: 179 TYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISC 238
Query: 131 -----CEICNFKYKFKRTLKRPLWETMAGWLYKVVENSQVFIILSWLMAITPIVLLAAAL 185
++ ++ K P ++ L + ++ A A+
Sbjct: 239 PLIGVIQLAHYVVTAKLLGFTP---------------GELRSYLKGATGHSQGLVTAVAI 283
>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 81
Score = 32.9 bits (75), Expect = 0.018
Identities = 10/61 (16%), Positives = 24/61 (39%), Gaps = 5/61 (8%)
Query: 85 DENAPVCRICHGSHENLKALCECRGTMGLVHAECLTQWLSESGRSCCEICNFKYKFKRTL 144
+ C+ + + + EC + H C++ W+ + + C +C + +R
Sbjct: 26 MDACLRCQAENKQEDCVVVWGECNHSF---HNCCMSLWVKQ--NNRCPLCQQDWVVQRIG 80
Query: 145 K 145
K
Sbjct: 81 K 81
>3nw0_A Non-structural maintenance of chromosomes element homolog; E3
ligase, Zn, metal binding protein; 2.92A {Homo sapiens}
Length = 238
Score = 34.3 bits (78), Expect = 0.036
Identities = 11/54 (20%), Positives = 20/54 (37%), Gaps = 3/54 (5%)
Query: 82 SEHDENAPVCRICHGSHENLKALCECRGTMGLVHAECLTQWLSESGRSCCEICN 135
+ + +C ICH ++ C M H C+ ++ + C CN
Sbjct: 174 ETYPDAVKICNICHSLLIQGQSCETCGIRM---HLPCVAKYFQSNAEPRCPHCN 224
>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 = 31.7 bits (71), Expect = 0.088
Identities = 18/82 (21%), Positives = 22/82 (26%), Gaps = 17/82 (20%)
Query: 64 SICNDILQLLEGEIDEIGSEHDENAPVCRICHGSHENLKALCECRGTMGLVHAECLTQWL 123
IC + L + G D S+ V R+ SH H CL
Sbjct: 29 IICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSH--------------AFHLLCLLAMY 74
Query: 124 SES---GRSCCEICNFKYKFKR 142
G C C Y K
Sbjct: 75 CNGNKDGSLQCPSCKTIYGEKT 96
>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila
melanogaster}
Length = 381
Score = 31.0 bits (69), Expect = 0.53
Identities = 12/56 (21%), Positives = 15/56 (26%), Gaps = 4/56 (7%)
Query: 78 DEIGSEHDENAPVCRIC----HGSHENLKALCECRGTMGLVHAECLTQWLSESGRS 129
E D C IC E C+ + HA CL +W
Sbjct: 298 GPKLDEEDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDG 353
>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein
of testis, proliferation potential-related protein,
protein P2P-R; NMR {Homo sapiens}
Length = 74
Score = 28.2 bits (63), Expect = 0.78
Identities = 13/60 (21%), Positives = 19/60 (31%), Gaps = 9/60 (15%)
Query: 91 CRICHGSHENLKALCECRGTMGLVHA---ECLTQWLSESGRSCCEICNFKYKFKRTLKRP 147
C IC + + C ++ EC+ L ES C C+ L P
Sbjct: 18 CLICKDIMTDAVVIPCCG------NSYCDECIRTALLESDEHTCPTCHQNDVSPDALSGP 71
>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 = 28.1 bits (62), Expect = 0.99
Identities = 15/63 (23%), Positives = 19/63 (30%), Gaps = 1/63 (1%)
Query: 73 LEGEIDEIGSEHDENAPVCRICH-GSHENLKALCECRGTMGLVHAECLTQWLSESGRSCC 131
G + VC IC G +N + C VH EC G+ C
Sbjct: 10 STGGSSGSSQSLIDEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLC 69
Query: 132 EIC 134
C
Sbjct: 70 RHC 72
>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 = 28.0 bits (62), Expect = 1.7
Identities = 13/63 (20%), Positives = 19/63 (30%), Gaps = 10/63 (15%)
Query: 81 GSEHDENAPVCRICHGSHENLKALCECRGTMGLVHAECLTQWLSESGRS--------CCE 132
GS A C +C + L C H CL ++ R+ C+
Sbjct: 1 GSSGSSGA-NCAVCDSPGDLLDQFF-CTTCGQHYHGMCLDIAVTPLKRAGWQCPECKVCQ 58
Query: 133 ICN 135
C
Sbjct: 59 NCK 61
>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1;
RCHY1, ring domain, zinc-binding domain, structural
genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A
Length = 55
Score = 26.1 bits (58), Expect = 3.0
Identities = 12/59 (20%), Positives = 20/59 (33%), Gaps = 11/59 (18%)
Query: 81 GSEHDENAPVCRICHGSHENLKALCECRGTMG---LVHAECLTQWLSESGRSCCEICNF 136
GS P+C E++ + L+H C + L E C +C+
Sbjct: 1 GSSGSSGCPIC------LEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEG--YRCPLCSG 51
>1pii_A N-(5'phosphoribosyl)anthranilate isomerase; bifunctional(isomerase
and synthase); 2.00A {Escherichia coli} SCOP: c.1.2.4
c.1.2.4 PDB: 1jcm_P* 2kzh_A
Length = 452
Score = 28.4 bits (64), Expect = 3.1
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 10/41 (24%)
Query: 212 MIRKDSCPISITPIYEGYAMIRKDSCPISI-TPIYEGKYFK 251
+IR D P I IY+ YA S IS+ T + KYF+
Sbjct: 63 VIRDDFDPARIAAIYKHYA-----SA-ISVLT---DEKYFQ 94
>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2,
protein structure initiative, northeast structural
genomics consortium, NESG; HET: MSE; 2.29A {Homo
sapiens}
Length = 100
Score = 26.4 bits (58), Expect = 4.7
Identities = 10/41 (24%), Positives = 15/41 (36%), Gaps = 5/41 (12%)
Query: 91 CRICHGSHENLKALCECRGTMG-LVHAECLTQWLSESGRSC 130
C IC + + C L C+ +WL+E C
Sbjct: 25 CFICMEKLRDARLCPHC----SKLCCFSCIRRWLTEQRAQC 61
>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus
interaction, receptor, UBL conjugation, UBL conjugation
pathway, acetylation, cytoplasm; 2.60A {Homo sapiens}
SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 1u6g_B 2hye_D* 4a0c_D
4a0l_F* 1ldj_B 1ldk_C 2lgv_A
Length = 106
Score = 26.3 bits (57), Expect = 5.8
Identities = 12/70 (17%), Positives = 24/70 (34%), Gaps = 13/70 (18%)
Query: 84 HDENAPVCRICHGSHENLKALCECRGTMGLV-----------HAECLTQWLSESGRSCCE 132
+N +CR + T H C+++WL R C
Sbjct: 36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT--RQVCP 93
Query: 133 ICNFKYKFKR 142
+ N +++F++
Sbjct: 94 LDNREWEFQK 103
>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin
ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB:
2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A
2ldr_A*
Length = 389
Score = 27.4 bits (60), Expect = 6.2
Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 4/58 (6%)
Query: 73 LEGEIDEIGSEHDENAPVCRICHGSHENLKALCECRGTMGLVHAECLTQWLSESGRSC 130
+ E E+ E +C+IC + +++K C M CLT W G+ C
Sbjct: 317 VTQEQYELYCEMGSTFQLCKICAENDKDVKIEP-CGHLM---CTSCLTSWQESEGQGC 370
>2vrq_A Alpha-L-arabinofuranosidase; hydrolase, glycosidase; HET: XYP;
2.00A {Thermobacillus xylanilyticus} PDB: 2vrk_A
Length = 496
Score = 27.5 bits (60), Expect = 6.7
Identities = 12/54 (22%), Positives = 22/54 (40%)
Query: 181 LAAALTNNFPFNHNDRKTHQQLQCGFDVRYAMIRKDSCPISITPIYEGYAMIRK 234
L A T + H DR + +V ++I + + +TP Y + M +
Sbjct: 324 LVAGATLHIFHRHCDRVRMANIAQLVNVLQSVILTEGERMLLTPTYHVFNMFKV 377
>3a1b_A DNA (cytosine-5)-methyltransferase 3A, histone H3; zinc-finger,
histone binding, chromosomal protein, DNA damag repair,
DNA-binding, methylation; HET: DNA; 2.29A {Homo sapiens}
PDB: 3a1a_A*
Length = 159
Score = 26.7 bits (58), Expect = 6.9
Identities = 15/75 (20%), Positives = 22/75 (29%), Gaps = 10/75 (13%)
Query: 83 EHDENAPVCRICHGSHENLKALCECRGTMGLVHAECLTQWLSESGRSC--------CEIC 134
+ D C IC G E L +C EC+ + C +C
Sbjct: 74 DDDGYQSYCTICCGGREVL--MCGNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMC 131
Query: 135 NFKYKFKRTLKRPLW 149
K + +R W
Sbjct: 132 GHKGTYGLLRRREDW 146
>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA
complex, DNA-binding protein- complex; HET: DNA 3DR;
5.93A {Mus musculus}
Length = 117
Score = 26.0 bits (56), Expect = 8.6
Identities = 12/69 (17%), Positives = 24/69 (34%), Gaps = 13/69 (18%)
Query: 85 DENAPVCRICHGSHENLKALCECRGTMGLV-----------HAECLTQWLSESGRSCCEI 133
+N +CR + T H C+++WL R C +
Sbjct: 48 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT--RQVCPL 105
Query: 134 CNFKYKFKR 142
N +++F++
Sbjct: 106 DNREWEFQK 114
>1n7o_A Hyaluronidase; protein mutant, lyase; 1.50A {Streptococcus
pneumoniae} SCOP: a.102.3.2 b.24.1.1 b.30.5.2 PDB:
1egu_A 1c82_A 1f9g_A* 1ojp_A* 1w3y_A* 2brp_A* 2brv_X
2brw_A 1lxk_A* 1loh_A* 1ojm_A* 1n7p_A 1ojn_A* 1n7n_A
1ojo_A* 1n7r_A* 1n7q_A*
Length = 721
Score = 27.0 bits (59), Expect = 9.7
Identities = 6/34 (17%), Positives = 14/34 (41%)
Query: 251 KNMRTQVLSQLVWYYDMLFMIVRAYFENWHFYYI 284
+ + V + W + ++ ++ NW Y I
Sbjct: 94 ETVVRTVRDSMEWMHKHVYNSEKSIVGNWWDYEI 127
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
0.323 0.137 0.433
Gapped
Lambda K H
0.267 0.0475 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,728,281
Number of extensions: 270528
Number of successful extensions: 736
Number of sequences better than 10.0: 1
Number of HSP's gapped: 725
Number of HSP's successfully gapped: 53
Length of query: 306
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 213
Effective length of database: 4,105,140
Effective search space: 874394820
Effective search space used: 874394820
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 57 (26.4 bits)