RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8979
(142 letters)
>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 = 35.2 bits (80), Expect = 0.005
Identities = 21/133 (15%), Positives = 45/133 (33%), Gaps = 24/133 (18%)
Query: 13 HHL-----KERLHYELEILMAYQSKNKMQAEAQRNRERKELEDRVSVRRALLEQKMDMET 67
HH+ + + Y+ +IL ++ N + K+++D + L ++++D
Sbjct: 5 HHMDFETGEHQYQYK-DILSVFEDAFV------DNFDCKDVQD--MPKSILSKEEIDHII 55
Query: 68 QQFLGERQERIR----LLHERQERELESFDQESNRMGFSALAIAEASKESYPDMDGSLSG 123
+ L +QE ++ F +E R+ + L S S+
Sbjct: 56 MS--KDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFL----MSPIKTEQRQPSMMT 109
Query: 124 SMLSLNHSNSCNS 136
M N
Sbjct: 110 RMYIEQRDRLYND 122
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 31.3 bits (70), Expect = 0.063
Identities = 10/73 (13%), Positives = 29/73 (39%), Gaps = 8/73 (10%)
Query: 33 NKMQAEAQ-----RNRERKELEDR---VSVRRALLEQKMDMETQQFLGERQERIRLLHER 84
+++ E + R +RK L++ V +K + +++ + E++
Sbjct: 78 DRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKIN 137
Query: 85 QERELESFDQESN 97
++F Q+ +
Sbjct: 138 NRIADKAFYQQPD 150
Score = 28.2 bits (62), Expect = 0.69
Identities = 11/39 (28%), Positives = 15/39 (38%)
Query: 76 ERIRLLHERQERELESFDQESNRMGFSALAIAEASKESY 114
E IR E Q + L+ D S M A+ E +
Sbjct: 85 ESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEW 123
Score = 26.3 bits (57), Expect = 3.6
Identities = 7/50 (14%), Positives = 17/50 (34%), Gaps = 1/50 (2%)
Query: 3 RLDESQEVECHHLKERLHYELEILMA-YQSKNKMQAEAQRNRERKELEDR 51
LD + +V +E+ +LE + + R ++ +
Sbjct: 100 ELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAFYQQP 149
>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex,
cytoplasm, ribonucleoprotein, structural protein; 3.50A
{Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A
Length = 861
Score = 30.5 bits (68), Expect = 0.16
Identities = 18/107 (16%), Positives = 38/107 (35%), Gaps = 2/107 (1%)
Query: 6 ESQEVECHHLKERLHYELEILMAYQSKNKMQAEAQRNRERKELEDRVSVRRALLEQKMDM 65
E Q++ E+ EL L A + A+ E + R+ ++L+ K+
Sbjct: 689 ERQKILDQSEAEKARKELLELEAMSMAVESTGNAKAEAESRAEAARIEGEGSVLQAKLKA 748
Query: 66 ETQQFLGERQERIRLLHERQERELESFDQESNRMGFSALAIAEASKE 112
+ E + + + + +E EL + A +A +
Sbjct: 749 QALAI--ETEAELERVKKVREMELIYARAQLELEVSKAQQLANVEAK 793
Score = 26.3 bits (57), Expect = 4.2
Identities = 15/77 (19%), Positives = 29/77 (37%), Gaps = 6/77 (7%)
Query: 36 QAEAQRNRERKELEDRVSVRRALLEQKMDMETQQFLGERQERIRLLHERQERELESFDQE 95
Q + +E + +R E + +E Q+ L + + E+ +EL +
Sbjct: 659 QLAIEITTNSQEAAAKHEAQRLEQEARGRLERQKILDQSEA------EKARKELLELEAM 712
Query: 96 SNRMGFSALAIAEASKE 112
S + + A AEA
Sbjct: 713 SMAVESTGNAKAEAESR 729
>3lpj_A Beta-secretase 1; alzheimer'S, aspartyl protease, hydrolase; HET:
TLA Z75; 1.79A {Homo sapiens} PDB: 3lpi_A* 3lpk_A*
3ohf_A* 3ohh_A* 3r2f_A* 3skf_A* 3skg_A* 2hiz_A* 2p83_A*
2va7_A* 2va5_A* 2va6_A*
Length = 455
Score = 29.5 bits (66), Expect = 0.37
Identities = 9/50 (18%), Positives = 21/50 (42%), Gaps = 4/50 (8%)
Query: 92 FDQESNRMGFSALAIAEASKESYPDMDGSLSGSMLSLNHSNSCNSFPEGS 141
FD+ R+GF+ A + ++ G ++L+ + + P+
Sbjct: 407 FDRARKRIGFAVSACHVHDEFR----TAAVEGPFVTLDMEDCGYNIPQTD 452
>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding,
nucleotide-binding, phosphorylation, acetylation,
alternative splicing, coiled coil; HET: GDP GTP; 4.00A
{Homo sapiens}
Length = 427
Score = 28.6 bits (63), Expect = 0.66
Identities = 12/66 (18%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 26 LMAYQSKNKMQAEAQRNRERKELEDRVSVRRALLEQKMDMETQQFLGERQERIRLLHERQ 85
L + + + ++ +E+ R E ++ E ++ L E+ +R++ LH+ +
Sbjct: 320 LQETYEAKRNEFLGELQKKEEEMRQMFVQRVKEKEAEL-KEAEKELHEKFDRLKKLHQDE 378
Query: 86 ERELES 91
+++LE
Sbjct: 379 KKKLED 384
Score = 26.6 bits (58), Expect = 3.2
Identities = 10/69 (14%), Positives = 24/69 (34%)
Query: 31 SKNKMQAEAQRNRERKELEDRVSVRRALLEQKMDMETQQFLGERQERIRLLHERQERELE 90
+ +R E + + + Q ++ E +E + LHE+ +R +
Sbjct: 314 DSKPFSLQETYEAKRNEFLGELQKKEEEMRQMFVQRVKEKEAELKEAEKELHEKFDRLKK 373
Query: 91 SFDQESNRM 99
E ++
Sbjct: 374 LHQDEKKKL 382
>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP
hydrolysis, GDP, GMP, dynamin related, large GTPase
family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens}
SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A*
2bc9_A* 2d4h_A*
Length = 592
Score = 28.8 bits (63), Expect = 0.67
Identities = 18/94 (19%), Positives = 40/94 (42%)
Query: 6 ESQEVECHHLKERLHYELEILMAYQSKNKMQAEAQRNRERKELEDRVSVRRALLEQKMDM 65
+++E+ +LK + IL Q+ + + E + R + E + +++K +
Sbjct: 456 QAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQ 515
Query: 66 ETQQFLGERQERIRLLHERQERELESFDQESNRM 99
+Q QE ++ L E+ E + +E R
Sbjct: 516 MMEQKERSYQEHLKQLTEKMENDRVQLLKEQERT 549
>2qp8_A Beta-secretase 1; BACE1, protease, alternative splicing, aspartyl
protease, glycoprotein, hydrolase, membrane,
transmembrane, zymogen; HET: TAR SC7; 1.50A {Homo
sapiens} SCOP: b.50.1.2 PDB: 2qk5_A* 2qmf_A* 2qmg_A*
2qmd_A* 4djx_A* 3l59_A* 3l5b_A* 3l5c_A* 3l58_A* 3l5d_A*
3l5f_A* 4dju_A* 4djv_A* 4djw_A* 3l5e_A* 4djy_A* 2zhv_A
2zhs_A 2zhr_A 2zhu_A ...
Length = 395
Score = 27.9 bits (62), Expect = 1.4
Identities = 7/33 (21%), Positives = 13/33 (39%)
Query: 92 FDQESNRMGFSALAIAEASKESYPDMDGSLSGS 124
FD+ R+GF+ A + ++G
Sbjct: 354 FDRARKRIGFAVSACHVHDEFRTAAVEGPFVTL 386
>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp
contractIle protein-transport protein complex; 24.00A
{Gallus gallus}
Length = 1080
Score = 27.8 bits (62), Expect = 1.4
Identities = 13/92 (14%), Positives = 37/92 (40%), Gaps = 2/92 (2%)
Query: 9 EVECHHLKERLHYELEILMAYQSKNKMQAEAQRNRERKELEDRVSVRRALLEQKMDMETQ 68
E + L+ ++ + + + K E + E ++L V R E+ + +
Sbjct: 927 ENKIMQLQRKIDEQNKEYKSLLEK-MNNLEITYSTETEKLRSDVERLRMSEEEAKNATNR 985
Query: 69 -QFLGERQERIRLLHERQERELESFDQESNRM 99
L E ++R + + E ++ ++ +++
Sbjct: 986 VLSLQEEIAKLRKELHQTQTEKKTIEEWADKY 1017
Score = 26.6 bits (59), Expect = 3.8
Identities = 16/94 (17%), Positives = 33/94 (35%), Gaps = 5/94 (5%)
Query: 6 ESQEVECHHLKERLHYELEILMAYQSKNKMQAEAQRNRERKELEDRVSVRRALLEQKMDM 65
E E + R+ L+ +A K Q E+K +E+ + EQ +
Sbjct: 973 RMSEEEAKNATNRVL-SLQEEIAKLRKEL----HQTQTEKKTIEEWADKYKHETEQLVSE 1027
Query: 66 ETQQFLGERQERIRLLHERQERELESFDQESNRM 99
+Q + E+ L ++ E + ++
Sbjct: 1028 LKEQNTLLKTEKEELNRRIHDQAKEITETMEKKL 1061
Score = 26.6 bits (59), Expect = 3.8
Identities = 14/79 (17%), Positives = 34/79 (43%), Gaps = 4/79 (5%)
Query: 6 ESQEVECHHLKE---RLHYELEILMAYQSKNKMQAEAQRNRERKELEDRVSVRRALLEQK 62
+ E ++E + +E E L++ + + ++ + + D+ +E+K
Sbjct: 1001 HQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQAKEITETMEKK 1060
Query: 63 MDMETQQFLGE-RQERIRL 80
+ ET+Q + ER+R
Sbjct: 1061 LVEETKQLELDLNDERLRY 1079
Score = 25.5 bits (56), Expect = 9.4
Identities = 14/87 (16%), Positives = 35/87 (40%), Gaps = 2/87 (2%)
Query: 6 ESQEVECHHLKERLHYELEILMAYQSK-NKMQAE-AQRNRERKELEDRVSVRRALLEQKM 63
S + E L++ LH + +K + E Q E KE + + L +++
Sbjct: 987 LSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRRI 1046
Query: 64 DMETQQFLGERQERIRLLHERQERELE 90
+ ++ ++++ ++ E +L
Sbjct: 1047 HDQAKEITETMEKKLVEETKQLELDLN 1073
>1rq0_A RF-1, peptide chain release factor 1; X-RAY, crystal, peptide
release factor 1, ribosome, structural genomics, BSGC
structure funded by NIH; 2.65A {Thermotoga maritima}
SCOP: e.38.1.1 PDB: 2fvo_A
Length = 342
Score = 27.2 bits (61), Expect = 1.9
Identities = 14/78 (17%), Positives = 34/78 (43%), Gaps = 6/78 (7%)
Query: 15 LKERLHYELEILMAYQS--KNKMQAEAQRNRERKELEDRVSVRRALLEQKMDMETQQFLG 72
+KE+ E+E L+A +M+ E ++E+ ++ + E + +E + G
Sbjct: 1 MKEK-KKEIEKLLARPDLTPEQMK---NYGMEYAKIEEIENITNRIKETQEFIELLREEG 56
Query: 73 ERQERIRLLHERQERELE 90
E + I + ++ +
Sbjct: 57 ENELEIEKYEKELDQLYQ 74
>2ycu_A Non muscle myosin 2C, alpha-actinin; motor protein; HET: AOV; 2.25A
{Homo sapiens} PDB: 1br1_A* 1br4_A* 1br2_A*
Length = 995
Score = 27.3 bits (61), Expect = 2.0
Identities = 11/97 (11%), Positives = 25/97 (25%), Gaps = 1/97 (1%)
Query: 1 MIRLDESQEVECHHLKERLHYELEILMAYQSKNKMQAEAQRNRERKELEDRVSVRRALLE 60
+ ++ +L LE + Q+ + +L + L
Sbjct: 899 VYLGSNETGDSITAVQAKLK-NLEAFDGECQSLEGQSNSDLLSILAQLTELNYNGVPELT 957
Query: 61 QKMDMETQQFLGERQERIRLLHERQERELESFDQESN 97
++ D Q + ELE + +
Sbjct: 958 ERKDTFFAQQWTGVKSSAETYKNTLLAELERLQKIED 994
Score = 25.4 bits (56), Expect = 8.0
Identities = 16/98 (16%), Positives = 36/98 (36%), Gaps = 7/98 (7%)
Query: 22 ELEILMAYQSKNKMQAEAQRNRERKELEDRVSVRRALLEQKMDMET-----QQFLGERQE 76
+ E Q ++++A + + L R ++++ ++ E E
Sbjct: 805 KTEKPPKGQEVSELEAIYNSLQTKLRLIKREPFVAPAGLTPNEIDSTWSALEKAEQEHAE 864
Query: 77 RIRLLHERQERELESFDQESNRMGFSALAIAEASKESY 114
+R+ +RQ++ Q+ NR L +K Y
Sbjct: 865 ALRIELKRQKKIAVLL-QKYNR-ILKKLENWATTKSVY 900
>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM,
protein engineering, structural protein; HET: ADP; 2.80A
{Dictyostelium discoideum} SCOP: k.1.1.1
Length = 1010
Score = 26.9 bits (60), Expect = 3.0
Identities = 10/98 (10%), Positives = 28/98 (28%), Gaps = 7/98 (7%)
Query: 2 IRLDESQEVECHHLKERLHYELEILMAYQSKNKMQAEAQRNRERKELEDRVSVRRALLEQ 61
+ L ++ + + LE + Q+ + +L + L
Sbjct: 907 VYLGSNETGDSITAVQAKLKNLEAFDGECQSLEGQSNSDLLSILAQLTE-------LNYN 959
Query: 62 KMDMETQQFLGERQERIRLLHERQERELESFDQESNRM 99
+ T++ ++ + E + E R+
Sbjct: 960 GVPELTERKDTFFAQQWTGVKSSAETYKNTLLAELERL 997
>1gqe_A Release factor 2, RF2; protein synthesis, ribosome, macromolecular
mimicry, translation; 1.81A {Escherichia coli} SCOP:
e.38.1.1 PDB: 1mi6_A 1ml5_Z*
Length = 365
Score = 26.5 bits (59), Expect = 3.7
Identities = 18/91 (19%), Positives = 34/91 (37%), Gaps = 3/91 (3%)
Query: 15 LKERLHYELEILMAYQSKNKMQAEAQR-NRERKELEDRVSVRRALLEQKMDMETQQFLGE 73
KERL E+ + AQ +ER LE V + + D+ L
Sbjct: 30 KKERLE-EVNAELEQPDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAV 88
Query: 74 RQERIRLLHERQERELESFDQESNRMGFSAL 104
+ +E EL++ +++ ++ F +
Sbjct: 89 EADDEETFNE-AVAELDALEEKLAQLEFRRM 118
>1lbq_A Ferrochelatase; rossmann fold, PI-helix, lyase; 2.40A
{Saccharomyces cerevisiae} SCOP: c.92.1.1 PDB: 1l8x_A
Length = 362
Score = 26.4 bits (59), Expect = 3.9
Identities = 4/26 (15%), Positives = 12/26 (46%), Gaps = 4/26 (15%)
Query: 11 ECHH----LKERLHYELEILMAYQSK 32
E + ++L ++ + +QS+
Sbjct: 220 EVAATVYNIMQKLKFKNPYRLVWQSQ 245
>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 = 26.6 bits (58), Expect = 4.1
Identities = 20/138 (14%), Positives = 41/138 (29%), Gaps = 59/138 (42%)
Query: 46 KELEDRVSVRRALLEQKMDMETQQ--------------------FLGERQERIR-----L 80
+L + + + D + F GE+ +RIR +
Sbjct: 1633 MDLYKTSKAAQDVWNR-ADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAM 1691
Query: 81 LHE-------RQERELESFDQESNRMGFSA----L--------AIAEASKESYPDM---- 117
+ E + E+ + ++ S F + L A+ K ++ D+
Sbjct: 1692 IFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKG 1751
Query: 118 ----DGSLSGSMLSLNHS 131
D + +G HS
Sbjct: 1752 LIPADATFAG------HS 1763
>2q24_A Putative TETR family transcriptional regulator; structural
genomics, PSI, protein structure initiative; 1.80A
{Streptomyces coelicolor A3}
Length = 194
Score = 25.8 bits (57), Expect = 5.0
Identities = 8/19 (42%), Positives = 15/19 (78%)
Query: 27 MAYQSKNKMQAEAQRNRER 45
M+ +K ++A+AQRNR++
Sbjct: 1 MSDATKRPLRADAQRNRDK 19
>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment
2, heavy meromyosin, essential light chain, motor
protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1
PDB: 3j04_A 3dtp_B 3dtp_A
Length = 1184
Score = 26.3 bits (58), Expect = 5.0
Identities = 14/92 (15%), Positives = 42/92 (45%), Gaps = 2/92 (2%)
Query: 9 EVECHHLKERLHYELEILMAYQSKNKMQAEAQRNRERKELEDRVSVRRALLEQKMDMETQ 68
E H ++ R+ E E Q++ K + + Q ++LE+ + R+ L +K+ + +
Sbjct: 926 EEILHEMEARIEEEEERSQQLQAEKK-KMQQQMLDLEEQLEEEEAARQKLQLEKVTADGK 984
Query: 69 -QFLGERQERIRLLHERQERELESFDQESNRM 99
+ + + + + + +E + ++ + +
Sbjct: 985 IKKMEDDILIMEDQNNKLTKERKLLEERVSDL 1016
Score = 25.6 bits (56), Expect = 7.7
Identities = 20/101 (19%), Positives = 41/101 (40%), Gaps = 9/101 (8%)
Query: 3 RLDESQEVECHHLKERLHYELEILMAYQSKNKMQAEAQRNRERKELEDRVSVRRALLEQK 62
++ E E L E++ EL+ +A + E + LED S + L++
Sbjct: 1060 KIKRKLEGESSDLHEQIA-ELQAQIAELKAQLAKKEEELQAALARLEDETSQKNNALKKI 1118
Query: 63 MDMETQ------QFLGERQERIRLLHERQE--RELESFDQE 95
++E+ E+ R + ++++ ELE+ E
Sbjct: 1119 RELESHISDLQEDLESEKAARNKAEKQKRDLSEELEALKTE 1159
>3pmr_A Amyloid-like protein 1; heparin binding, cell adhesion; 2.11A {Homo
sapiens} PDB: 3q7l_A 3q7g_A 3qmk_A*
Length = 219
Score = 25.6 bits (55), Expect = 6.5
Identities = 15/76 (19%), Positives = 31/76 (40%)
Query: 13 HHLKERLHYELEILMAYQSKNKMQAEAQRNRERKELEDRVSVRRALLEQKMDMETQQFLG 72
L+ER ++ +M + Q++ +R+ L + LE+++ E Q+ +
Sbjct: 35 MDLEERRMRQINEVMREWAMADNQSKNLPKADRQALNEHFQSILQTLEEQVSGERQRLVE 94
Query: 73 ERQERIRLLHERQERE 88
R+ L Q R
Sbjct: 95 THATRVIALINDQRRA 110
>3umh_A Amyloid beta A4 protein; metal binding site, metal binding, cell
surface, secretory P metal binding protein; 2.00A {Homo
sapiens} PDB: 3umi_A 3umk_A 1rw6_A 3nyl_A 3nyj_A 1tkn_A
Length = 211
Score = 25.2 bits (54), Expect = 7.3
Identities = 13/75 (17%), Positives = 29/75 (38%)
Query: 14 HLKERLHYELEILMAYQSKNKMQAEAQRNRERKELEDRVSVRRALLEQKMDMETQQFLGE 73
L+ + + +M + + QA+ ++K + + LEQ+ E QQ +
Sbjct: 29 RLEAKHRERMSQVMREWEEAERQAKNLPKADKKAVIQHFQEKVESLEQEAANERQQLVET 88
Query: 74 RQERIRLLHERQERE 88
R+ + + R
Sbjct: 89 HMARVEAMLNDRRRL 103
>3hcn_A Ferrochelatase, mitochondrial; metal selectivity, disease mutation,
heme biosynthesis, iron, iron-sulfur, lyase, membrane,
metal-BIN mitochondrion; HET: CHD HEM GOL; 1.60A {Homo
sapiens} PDB: 2qd3_A* 2qd5_A* 2qd4_A* 3hco_A* 3hcr_A*
2qd1_A* 2hre_A* 3hcp_A* 2qd2_A* 2hrc_A* 1hrk_A* 3aqi_A*
2pnj_A* 2po5_A* 2po7_A*
Length = 359
Score = 25.6 bits (57), Expect = 7.7
Identities = 8/26 (30%), Positives = 11/26 (42%), Gaps = 4/26 (15%)
Query: 11 ECHH----LKERLHYELEILMAYQSK 32
E + ERL Y + +QSK
Sbjct: 215 EVSATVQKVMERLEYCNPYRLVWQSK 240
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
0.313 0.127 0.338
Gapped
Lambda K H
0.267 0.0439 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,056,877
Number of extensions: 111339
Number of successful extensions: 413
Number of sequences better than 10.0: 1
Number of HSP's gapped: 392
Number of HSP's successfully gapped: 108
Length of query: 142
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 58
Effective length of database: 4,356,429
Effective search space: 252672882
Effective search space used: 252672882
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.5 bits)