RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12380
(342 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 = 44.8 bits (105), Expect = 3e-05
Identities = 34/245 (13%), Positives = 67/245 (27%), Gaps = 50/245 (20%)
Query: 66 DKSLNEQEPLTFFLLHYILFLFVWSYYKTTTTPPPPIPPDFFLSAATMNKIWEAD--ENC 123
+ SLN EP + + L +F PP + ++ IW +
Sbjct: 360 ESSLNVLEPAEYRKMFDRLSVF---------------PPSAHIPTILLSLIWFDVIKSDV 404
Query: 124 EKIDAILVPK---ARRLPIYTYTT-GGYIRYCQECAIIKPDRTHHCRVCGQCILKMDHHC 179
+ L ++ T + Y+ + + H R
Sbjct: 405 MVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLEN---EYALH-RSIVDHYNIPKTFD 460
Query: 180 PWLHNCMSFSNYKFYILFLAYGAIYCVIMLSILPIELYKYWWQDKVLD----EALLYHYT 235
Y FY + + + +I E ++ LD E + H +
Sbjct: 461 SDDLIPPYLDQY-FY-SHIGHH------LKNIEHPERMTL-FRMVFLDFRFLEQKIRHDS 511
Query: 236 ILSISAVIFFAILIALFSYHIYLVLNNRT------TLEAFRAPLFSYGQDKNGFSLGKRN 289
++ L L Y Y+ N+ + F L ++ K
Sbjct: 512 TAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDF---LPKIEEN---LICSKYT 565
Query: 290 NFLQV 294
+ L++
Sbjct: 566 DLLRI 570
>2oyn_A Hypothetical protein MJ0056; structural genomics, unknown function,
PSI-2, protein structure initiative; HET: CDP; 1.85A
{Methanocaldococcus jannaschii DSM2661} SCOP: b.43.5.2
PDB: 2p3m_A 2vbs_A 2vbt_A* 2vbu_A* 2vbv_A*
Length = 146
Score = 32.1 bits (73), Expect = 0.11
Identities = 13/63 (20%), Positives = 22/63 (34%), Gaps = 14/63 (22%)
Query: 112 TMNKIWEADENCEKIDAILVP----------KARRLPIYTYTTGGYIRYCQECAIIKPDR 161
T+N + + + K I + LPI I + AI+ P +
Sbjct: 45 TLNLKLDREFDINKFKYIETEDFEFNGKRFFGVKVLPIKILIGNKKI----DGAIVVPKK 100
Query: 162 THH 164
T+H
Sbjct: 101 TYH 103
>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 = 32.3 bits (73), Expect = 0.16
Identities = 12/49 (24%), Positives = 16/49 (32%), Gaps = 13/49 (26%)
Query: 151 CQECAIIKP----DRTHHCRVCGQCILKMDHHC----P-WLHNCMSFSN 190
C EC + P + VC C L + W +FSN
Sbjct: 24 CPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEW----RTFSN 68
>1joc_A EEA1, early endosomal autoantigen 1; FYVE domain, inositol
3-phosphate binding, membrane protein; HET: ITP; 2.20A
{Homo sapiens} SCOP: g.50.1.1 h.1.21.1 PDB: 1hyi_A*
1hyj_A
Length = 125
Score = 30.7 bits (69), Expect = 0.25
Identities = 11/41 (26%), Positives = 13/41 (31%), Gaps = 11/41 (26%)
Query: 151 CQECAII--KPDRTHHCRVCGQCILKMDHHCPWLHNCMSFS 189
C C R HHCR CG C C + +
Sbjct: 72 CMACGKGFSVTVRRHHCRQCGNI------FC---AECSAKN 103
>1x4u_A Zinc finger, FYVE domain containing 27 isoform B; phosphoinositide
binding, zinc binding, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 84
Score = 29.5 bits (66), Expect = 0.34
Identities = 6/25 (24%), Positives = 10/25 (40%), Gaps = 6/25 (24%)
Query: 151 CQECA----IIKPDRTHHCRVCGQC 171
C C+ ++K + C CG
Sbjct: 17 CTGCSATFSVLK--KRRSCSNCGNS 39
>2yw8_A RUN and FYVE domain-containing protein 1; structure genomics,
structural genomics, NPPSFA; 3.00A {Homo sapiens} PDB:
2yqm_A
Length = 82
Score = 29.3 bits (66), Expect = 0.38
Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 6/28 (21%)
Query: 148 IRYCQECA----IIKPDRTHHCRVCGQC 171
+C++C I + R HHCR CG
Sbjct: 19 ATHCRQCEKEFSISR--RKHHCRNCGHI 44
>3t7l_A Zinc finger FYVE domain-containing protein 16; structural genomics
consortium, SGC, lipid BIND protein, transport protein;
1.09A {Homo sapiens}
Length = 90
Score = 29.4 bits (66), Expect = 0.44
Identities = 7/11 (63%), Positives = 8/11 (72%)
Query: 161 RTHHCRVCGQC 171
R HHCR CG+
Sbjct: 35 RRHHCRACGKV 45
>1vfy_A Phosphatidylinositol-3-phosphate binding FYVE domain of protein
VPS27; endosome maturation, intracellular trafficking;
1.15A {Saccharomyces cerevisiae} SCOP: g.50.1.1
Length = 73
Score = 28.5 bits (64), Expect = 0.55
Identities = 9/25 (36%), Positives = 12/25 (48%), Gaps = 6/25 (24%)
Query: 151 CQECA----IIKPDRTHHCRVCGQC 171
C C+ ++ R HHCR CG
Sbjct: 14 CMICSKKFSLLN--RKHHCRSCGGV 36
>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania
major}
Length = 84
Score = 28.9 bits (65), Expect = 0.59
Identities = 9/28 (32%), Positives = 9/28 (32%), Gaps = 6/28 (21%)
Query: 148 IRYCQECA----IIKPDRTHHCRVCGQC 171
C C R HHCR CG
Sbjct: 21 APACNGCGCVFTTTV--RRHHCRNCGYV 46
>2dkt_A Ring finger and CHY zinc finger domain- containing protein 1;
RCHY1, structural genomics, NPPSFA; NMR {Mus musculus}
SCOP: g.89.1.1 g.93.1.1 PDB: 2k2c_A
Length = 143
Score = 29.7 bits (66), Expect = 0.64
Identities = 10/32 (31%), Positives = 13/32 (40%), Gaps = 3/32 (9%)
Query: 151 CQECAIIKPDRTHHCRVCGQCI---LKMDHHC 179
C C I + HC C C+ L+ H C
Sbjct: 104 CGICRIGPKEDFFHCLKCNLCLTTNLRGKHKC 135
>1hfe_L Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larger subunit));
hydrogene metabolism, periplasm; 1.60A {Desulfovibrio
vulgaris subsp} SCOP: c.96.1.1 d.58.1.5 PDB: 1e08_A*
1gx7_A*
Length = 421
Score = 30.8 bits (70), Expect = 0.70
Identities = 13/40 (32%), Positives = 15/40 (37%), Gaps = 11/40 (27%)
Query: 148 IRYCQECAIIKPDRTHH-------CRVCGQCILKMDHHCP 180
+YC AI H C CGQC+ HCP
Sbjct: 42 SQYCPTAAIFGEMGEPHSIPHIEACINCGQCL----THCP 77
>3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2, protein
structure initiative; 2.20A {Thermoplasma acidophilum
dsm 1728} SCOP: a.4.5.28 b.43.5.2
Length = 230
Score = 30.1 bits (67), Expect = 0.90
Identities = 5/12 (41%), Positives = 8/12 (66%)
Query: 153 ECAIIKPDRTHH 164
C +I P+RT +
Sbjct: 181 PCFVIMPERTVY 192
>1wfk_A Zinc finger, FYVE domain containing 19; riken structural
genomics/proteomics initiative, RSGI, structural
genomics, unknown function; NMR {Mus musculus} SCOP:
g.50.1.1
Length = 88
Score = 28.2 bits (63), Expect = 1.0
Identities = 7/25 (28%), Positives = 12/25 (48%), Gaps = 6/25 (24%)
Query: 151 CQECA----IIKPDRTHHCRVCGQC 171
C CA + K + + C+ CG+
Sbjct: 12 CYGCAVKFTLFK--KEYGCKNCGRA 34
>3zyq_A Hepatocyte growth factor-regulated tyrosine kinas substrate;
signaling; 1.48A {Homo sapiens} PDB: 4avx_A*
Length = 226
Score = 29.7 bits (66), Expect = 1.1
Identities = 10/25 (40%), Positives = 11/25 (44%), Gaps = 2/25 (8%)
Query: 149 RYCQECAII--KPDRTHHCRVCGQC 171
C C + R HHCR CGQ
Sbjct: 165 EECHRCRVQFGVMTRKHHCRACGQI 189
>1dvp_A HRS, hepatocyte growth factor-regulated tyrosine kinase substrate;
VHS, FYVE, zinc finger, superhelix, transferase; HET:
CIT; 2.00A {Drosophila melanogaster} SCOP: a.118.9.2
g.50.1.1
Length = 220
Score = 29.0 bits (64), Expect = 1.8
Identities = 11/25 (44%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 149 RYCQECAIIKP--DRTHHCRVCGQC 171
R C C + +R HHCR CGQ
Sbjct: 162 RVCHRCRVEFTFTNRKHHCRNCGQV 186
>2csz_A Synaptotagmin-like protein 4; exophilin 2, granuphilin, ring
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 76
Score = 26.5 bits (58), Expect = 3.5
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 149 RYCQECAIIKPDRTHHCRVCGQ 170
C++C I + + T C+VC
Sbjct: 51 LVCRDCRIQESNGTWRCKVCSG 72
>1qd5_A Outer membrane phospholipase A; anti-parallel beta barrel, membrane
protein; HET: BOG; 2.17A {Escherichia coli} SCOP:
f.4.2.1 PDB: 1fw2_A* 1fw3_A* 1ilz_A* 1ild_A* 1im0_A*
Length = 275
Score = 28.3 bits (63), Expect = 3.6
Identities = 5/37 (13%), Positives = 12/37 (32%)
Query: 274 FSYGQDKNGFSLGKRNNFLQVFGDKKWKWFFPVFSSL 310
Y S + N+ +G + +P+ +
Sbjct: 205 IGYHLGDAVLSAKGQYNWNTGYGGAELGLSYPITKHV 241
>2vrw_B P95VAV, VAV1, proto-oncogene VAV; lipoprotein, GTP-binding,
metal-binding, phosphoprotein, exchange factor, RAC,
GTPase, membrane domain; 1.85A {Mus musculus} PDB:
3bji_A 1f5x_A
Length = 406
Score = 28.3 bits (63), Expect = 4.0
Identities = 4/26 (15%), Positives = 9/26 (34%), Gaps = 3/26 (11%)
Query: 150 YCQECAII---KPDRTHHCRVCGQCI 172
C+ C ++ + + C C
Sbjct: 359 SCKACQMLLRGTFYQGYRCYRCRAPA 384
>1i1r_A GP130, interleukin-6 receptor beta chain; cytokine/receptor
complex, GP130; 2.40A {Homo sapiens} SCOP: b.1.2.1
b.1.2.1 b.1.2.1 PDB: 1p9m_A
Length = 303
Score = 28.3 bits (62), Expect = 4.3
Identities = 7/54 (12%), Positives = 15/54 (27%), Gaps = 9/54 (16%)
Query: 144 TGGYIRYCQECAIIKPDRTHHCRVCGQCILKMDHH--CPWLHNCMSFSNYKFYI 195
T + + C K D C ++ + F N + ++
Sbjct: 130 THLETNFTLKS-------EWATHKFADCKAKRDTPTSCTVDYSTVYFVNIEVWV 176
>1qd6_C Protein (outer membrane phospholipase (ompla)); anti-parallel beta
barrel dimer, membrane protein; HET: HDS; 2.10A
{Escherichia coli} SCOP: f.4.2.1
Length = 240
Score = 27.1 bits (60), Expect = 7.8
Identities = 5/37 (13%), Positives = 12/37 (32%)
Query: 274 FSYGQDKNGFSLGKRNNFLQVFGDKKWKWFFPVFSSL 310
Y S + N+ +G + +P+ +
Sbjct: 170 IGYHLGDAVLSAKGQYNWNTGYGGAELGLSYPITKHV 206
>2wjn_L Reaction center protein L chain; bacteriochlorophyll,
lipidic-sponge phase, photosynthesis, R center, electron
transport, cell membrane; HET: HEM FME BCB BPB MPG MQ7
NS5; 1.86A {Rhodopseudomonas viridis} PDB: 2wjm_L*
2x5u_L* 2x5v_L* 4ac5_L* 3t6e_L* 1r2c_L* 1prc_L* 1vrn_L*
2jbl_L* 2prc_L* 3d38_L* 3g7f_L* 3prc_L* 2i5n_L* 3t6d_L*
5prc_L* 6prc_L* 7prc_L* 1dxr_L*
Length = 274
Score = 27.3 bits (60), Expect = 8.1
Identities = 24/149 (16%), Positives = 43/149 (28%), Gaps = 22/149 (14%)
Query: 173 LKMDHHCPWLHNCMSFSNYKFYILFLAYGAIYCVIMLSILPIELYKYW----WQDKVLDE 228
L + H P F +F +++ S Y W + +
Sbjct: 112 LGIGWHVPLAFCVPIF-------MFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQ 164
Query: 229 ALLYHYTILSISAVIFFAILIALFSYH--IYLVLNNRTTLEAFRAPLF--SYGQDKNGFS 284
L +HY +S+V F + H + L + N + + Y +D G+S
Sbjct: 165 YLNWHYNPGHMSSVSFLFVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYS 224
Query: 285 LGKRNNFLQVFGDKKWKWFFPVFSSLGCG 313
+G + F L
Sbjct: 225 IGA-------LSIHRLGLFLASNIFLTGA 246
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 0.143 0.479
Gapped
Lambda K H
0.267 0.0515 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,518,753
Number of extensions: 321395
Number of successful extensions: 914
Number of sequences better than 10.0: 1
Number of HSP's gapped: 906
Number of HSP's successfully gapped: 32
Length of query: 342
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 248
Effective length of database: 4,077,219
Effective search space: 1011150312
Effective search space used: 1011150312
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 (21.7 bits)
S2: 58 (26.6 bits)