RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6472
(72 letters)
>2odv_A Plectin 1, HD1; plakin domain, spectrin repeat, cytoskeleton,
hemidesmosomes epidermolysis bullosa, structural
protein; 2.05A {Homo sapiens} PDB: 2odu_A
Length = 235
Score = 37.8 bits (87), Expect = 7e-05
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 4/74 (5%)
Query: 1 MKRVDGRLEELESRINEEARRL----DRLHPLDAKHNVDVLEHDLRQAEENINTLFSDVQ 56
+ ++ E ++N+ L L +E DL +A+ I LF+DVQ
Sbjct: 130 VTKLQMEAGLAEEQLNQADALLQSDVRLLAAGKVPQRAGEVERDLDKADSMIRLLFNDVQ 189
Query: 57 TLREGRYPQASDLH 70
TL++GR+PQ ++
Sbjct: 190 TLKDGRHPQGEQMY 203
>3gv2_A Ca, fusion protein consisting of capsid protein P24, linker and
carbon dioxide-concentrating...; hexameric retroviral
capsid; 7.00A {Human immunodeficiency virus type 1}
Length = 342
Score = 29.9 bits (67), Expect = 0.038
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 11 LESRINEEARRLDRLHPLDA 30
L+ INEEA DRLHP+ A
Sbjct: 69 LKETINEEAAEWDRLHPVHA 88
>1l6n_A GAG polyprotein; matrix, capsid, maturation, viral protein; NMR
{Human immunodeficiency virus 1} SCOP: a.61.1.1 a.73.1.1
Length = 289
Score = 29.6 bits (67), Expect = 0.054
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 11 LESRINEEARRLDRLHPLDA 30
L+ INEEA DRLHP+ A
Sbjct: 201 LKETINEEAAEWDRLHPVHA 220
>3h47_A Ca, capsid protein P24; hexamer, engineered disulfide bonds,
viral protein; 1.90A {Human immunodeficiency virus type
1} PDB: 3h4e_A 2lf4_A 3mge_A 3p05_A 3p0a_A 3dik_A
3nte_A 1e6j_P
Length = 231
Score = 29.4 bits (66), Expect = 0.057
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 11 LESRINEEARRLDRLHPLDA 30
L+ INEEA DRLHP+ A
Sbjct: 69 LKETINEEAAEWDRLHPVHA 88
>1eia_A EIAV capsid protein P26; viral capsid, HIV, lentivirus, viral
protein; 2.70A {Equine infectious anemia virus} SCOP:
a.28.3.1 a.73.1.1 PDB: 2eia_A
Length = 207
Score = 29.1 bits (65), Expect = 0.075
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 6 GRLEELESRINEEARRLDRLHPLDA 30
G+ + L I++ A D HPL
Sbjct: 50 GQKQILLDAIDKIADDWDNRHPLPN 74
>2wlv_A GAG polyprotein, HIV-2 capsid,; virus protein, RNA-binding,
capsid protein, viral nucleoprotein, AIDS; 1.25A {Human
immunodeficiency virus type 2} PDB: 2x82_A
Length = 144
Score = 28.3 bits (63), Expect = 0.14
Identities = 8/17 (47%), Positives = 9/17 (52%)
Query: 11 LESRINEEARRLDRLHP 27
+ INEEA D HP
Sbjct: 68 IREIINEEAAEWDVQHP 84
>2xde_A GAG polyprotein, HIV-1 capsid; AIDS, viral protein; HET: 1B0;
1.40A {Human immunodeficiency virus 1} PDB: 1m9y_C
2x2d_D* 1m9x_C 1m9e_C 1m9f_C 1afv_A 1gwp_A 2pxr_C
2gol_B 1m9c_C 2x83_A 4e91_A* 4e92_A* 2pwo_A 2pwm_A
2gon_A 1ak4_C 2jpr_A* 1m9d_C 4dga_C ...
Length = 145
Score = 27.9 bits (62), Expect = 0.16
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 11 LESRINEEARRLDRLHPL 28
L+ INEEA DRLHP+
Sbjct: 70 LKETINEEAAEWDRLHPV 87
>2xgu_A Relik capsid N-terminal domain; viral protein, retroviral capsid;
1.50A {Oryctolagus cuniculus} PDB: 2xgy_A
Length = 149
Score = 28.0 bits (62), Expect = 0.18
Identities = 6/17 (35%), Positives = 10/17 (58%)
Query: 11 LESRINEEARRLDRLHP 27
+ +I E+A D +HP
Sbjct: 69 VIDKIKEKAIAWDEMHP 85
>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 = 28.1 bits (62), Expect = 0.24
Identities = 10/55 (18%), Positives = 17/55 (30%), Gaps = 7/55 (12%)
Query: 9 EELESRINEEARRL----DRLHPLDAKHNVDVLEHDLRQAEENINTLF-SDVQTL 58
+E + + L + P VL L + E L +D+ L
Sbjct: 52 DEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCY--LEGNDIHAL 104
Score = 24.2 bits (52), Expect = 4.2
Identities = 15/76 (19%), Positives = 23/76 (30%), Gaps = 18/76 (23%)
Query: 8 LEELESRINEEARRLD-RLHPLDAK----HNVDVLEHDLRQAEENINTLFSDVQTLREGR 62
L IN++ + + + D + D DLR +I+ D R
Sbjct: 432 LVPASDLINKDLVKNNVSFNAKDIQIPVYDTFD--GSDLRVLSGSISERIVDCII----R 485
Query: 63 YP-------QASDLHI 71
P Q HI
Sbjct: 486 LPVKWETTTQFKATHI 501
>1mqm_B Hemagglutinin HA2 chain; influenza virus, viral protein; HET: NAG
BMA MAN SIA GAL; 2.60A {Influenza a virus} SCOP: h.3.1.1
PDB: 1mql_B* 1mqn_B* 2l4g_A
Length = 221
Score = 27.7 bits (61), Expect = 0.27
Identities = 14/64 (21%), Positives = 30/64 (46%), Gaps = 6/64 (9%)
Query: 3 RVDGRLEELESRINEEARRLDRLHPLDAKHNVDVL-----EHDLRQAEENINTLFSDVQ- 56
+++ E+E RI + + ++ +N ++L +H + A+ +N LF +
Sbjct: 65 QIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLADSEMNKLFEKTRR 124
Query: 57 TLRE 60
LRE
Sbjct: 125 QLRE 128
>2wr1_A Hemagglutinin; glycoprotein, lipoprotein, envelope protein, viral
protein; HET: SIA GAL NAG BMA MAN; 2.10A {Unidentified
influenza virus} PDB: 2wr0_A* 2wr2_A* 2wr3_A* 2wr4_A*
2wr5_A 2wrf_A* 2wr7_A* 2wrb_A* 2wrc_A 2wrd_A 2wre_A*
3gbm_A* 2fk0_A* 3s11_A* 3s13_A* 3s12_A* 3fku_A*
Length = 509
Score = 27.4 bits (60), Expect = 0.40
Identities = 13/64 (20%), Positives = 26/64 (40%), Gaps = 6/64 (9%)
Query: 3 RVDGRLEELESRINEEARRLDRLHPLDAKHNVDVL-----EHDLRQAEENINTLFSDVQ- 56
V LE R+ ++++ +N ++L E L + N+ L+ V+
Sbjct: 405 AVGKEFSNLERRLENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRM 464
Query: 57 TLRE 60
LR+
Sbjct: 465 QLRD 468
>3guy_A Short-chain dehydrogenase/reductase SDR; structural genomics,
oxidoreductase, PSI-2, protein structur initiative;
1.90A {Vibrio parahaemolyticus}
Length = 230
Score = 26.8 bits (60), Expect = 0.51
Identities = 7/30 (23%), Positives = 11/30 (36%), Gaps = 2/30 (6%)
Query: 19 ARRLDRLHPLDAK--HNVDVLEHDLRQAEE 46
R +L + +NV DL +E
Sbjct: 32 GRSESKLSTVTNCLSNNVGYRARDLASHQE 61
>1ha0_A Protein (hemagglutinin precursor); glycoprotein, membrane-fusion
precursor, virus/viral protein protein; HET: NAG BMA
MAN; 2.80A {Influenza a virus} SCOP: b.19.1.2 h.3.1.1
Length = 494
Score = 26.6 bits (58), Expect = 0.72
Identities = 14/65 (21%), Positives = 31/65 (47%), Gaps = 8/65 (12%)
Query: 3 RVDGRLEELESRINEEARRLDRLHPLDA-KHNVDVL-----EHDLRQAEENINTLFSDVQ 56
+++ E+E RI + + ++ +D +N ++L +H + + +N LF +
Sbjct: 386 QIEKEFSEVEGRIQDLEKYVED-TKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTR 444
Query: 57 -TLRE 60
LRE
Sbjct: 445 RQLRE 449
>3thx_B DNA mismatch repair protein MSH3; ABC family ATPase, mismatch
recognition, mismatched unpaired DNA binding protein-DNA
complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 3thw_B*
3thy_B* 3thz_B*
Length = 918
Score = 26.1 bits (58), Expect = 0.97
Identities = 12/50 (24%), Positives = 19/50 (38%)
Query: 2 KRVDGRLEELESRINEEARRLDRLHPLDAKHNVDVLEHDLRQAEENINTL 51
K+ + +ELE IN + +RL L HN L+ +
Sbjct: 868 KKAAHKSKELEGLINTKRKRLKYFAKLWTMHNAQDLQKWTEEFNMEETQT 917
>2wrg_I Hemagglutinin HA2 chain; viral protein, envelope protein,
glycoprotein, lipoprotein; HET: NAG SIA GAL; 3.00A
{Influenza a virus} PDB: 2wrh_I*
Length = 222
Score = 25.7 bits (56), Expect = 1.1
Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 6/64 (9%)
Query: 3 RVDGRLEELESRINEEARRLDRLHPLDAKHNVDVL-----EHDLRQAEENINTLFSDVQ- 56
V LE RI +++D +N ++L E L + N+ L+ V+
Sbjct: 65 AVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYEKVKS 124
Query: 57 TLRE 60
L+
Sbjct: 125 QLKN 128
>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 = 26.0 bits (56), Expect = 1.2
Identities = 13/67 (19%), Positives = 28/67 (41%), Gaps = 14/67 (20%)
Query: 6 GRLEELESRINEEARRLDRLHPLDAKHNVDVLEHDLRQAEEN-INTLFSDV-----QTLR 59
+L+ + I + + +RL V+ + L + EEN I + ++D+
Sbjct: 525 QQLKFYKPYICDNDPKYERL--------VNAILDFLPKIEENLICSKYTDLLRIALMAED 576
Query: 60 EGRYPQA 66
E + +A
Sbjct: 577 EAIFEEA 583
>3p19_A BFPVVD8, putative blue fluorescent protein; rossmann-fold,
oxidoreductase; HET: NAP; 2.05A {Vibrio vulnificus}
Length = 266
Score = 25.3 bits (56), Expect = 1.5
Identities = 8/28 (28%), Positives = 12/28 (42%), Gaps = 1/28 (3%)
Query: 19 ARRLDRLHPLDAKHNVDVLEHDLRQAEE 46
ARR++RL L N + D+
Sbjct: 47 ARRVERLKAL-NLPNTLCAQVDVTDKYT 73
>3e9n_A Putative short-chain dehydrogenase/reductase; structural
genomics, unknown function, oxidoreductase, PSI- 2;
2.40A {Corynebacterium glutamicum}
Length = 245
Score = 25.2 bits (56), Expect = 1.7
Identities = 6/28 (21%), Positives = 11/28 (39%)
Query: 19 ARRLDRLHPLDAKHNVDVLEHDLRQAEE 46
R + L L V+ +E D+ +
Sbjct: 35 GRNPEHLAALAEIEGVEPIESDIVKEVL 62
>3asu_A Short-chain dehydrogenase/reductase SDR; SDR family,
rossmann-fold, short-chain dehydrogenase/reducta
ALLO-threonine dehydrogenase; 1.90A {Escherichia coli}
PDB: 3asv_A*
Length = 248
Score = 24.8 bits (55), Expect = 2.8
Identities = 8/30 (26%), Positives = 14/30 (46%), Gaps = 2/30 (6%)
Query: 19 ARRLDRLHPLDAK--HNVDVLEHDLRQAEE 46
RR +RL L + N+ + + D+R
Sbjct: 31 GRRQERLQELKDELGDNLYIAQLDVRNRAA 60
>2nwq_A Probable short-chain dehydrogenase; oxidoreductase; 2.30A
{Pseudomonas aeruginosa}
Length = 272
Score = 24.5 bits (54), Expect = 3.2
Identities = 11/32 (34%), Positives = 13/32 (40%), Gaps = 4/32 (12%)
Query: 19 ARRLDRLHPL----DAKHNVDVLEHDLRQAEE 46
RR +RL L AK V L D+R
Sbjct: 52 GRREERLQALAGELSAKTRVLPLTLDVRDRAA 83
>2cyb_A Tyrosyl-tRNA synthetase; rossmann-fold, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; HET: TYR; 1.80A {Archaeoglobus
fulgidus}
Length = 323
Score = 24.5 bits (54), Expect = 3.7
Identities = 13/49 (26%), Positives = 17/49 (34%), Gaps = 15/49 (30%)
Query: 8 LEELESRINEEARRLDRLHPLDAKHNVDVLEHDLRQAEENINTLFSDVQ 56
EEL +LHPLD K V + +N L D +
Sbjct: 283 FEELAEDFKS-----GQLHPLDLKIAV----------AKYLNMLLEDAR 316
>3odn_A Dally-like protein; alpha helical bundle, hedgehog signaling,
hedgehog VIA CO- immunoprecipitation, membrane protein;
2.40A {Drosophila melanogaster}
Length = 506
Score = 24.1 bits (51), Expect = 4.7
Identities = 10/61 (16%), Positives = 25/61 (40%), Gaps = 3/61 (4%)
Query: 9 EELESRINEEARRLDRLHPLDAKHNVDVLEHDLRQAEENINTLFSDVQTLREGRYPQASD 68
++LE ++ R+ + A D+ L+++ N++F + Y + S
Sbjct: 60 QQLEGHTKDQISRMSGILGSKATKFKDIFTALLKESRTQFNSMFIRTYGV---IYERNSY 116
Query: 69 L 69
+
Sbjct: 117 V 117
>2rft_B Influenza B hemagglutinin (HA); viral protein, receptor
specificity, envelope Pro fusion protein, membrane,
transmembrane, VIR glycoprotein; HET: NAG SIA BGC GAL
NDG; 2.80A {Influenza b virus} SCOP: j.79.1.1 PDB:
2rfu_B* 3bt6_B*
Length = 176
Score = 23.8 bits (51), Expect = 5.7
Identities = 11/59 (18%), Positives = 26/59 (44%), Gaps = 5/59 (8%)
Query: 3 RVDGRLEELESRINEEARRLDRLHPLDAKHNVDVL-----EHDLRQAEENINTLFSDVQ 56
R+ G ++EL + I E ++D L +++ E + +E++ L ++
Sbjct: 65 RLSGAMDELHNEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLK 123
>1jsd_B Haemagglutinin (HA2 chain); viral protein; HET: NAG; 1.80A
{Influenza a virus} SCOP: h.3.1.1 PDB: 1jsh_B* 1jsi_B*
Length = 176
Score = 23.9 bits (51), Expect = 6.1
Identities = 13/59 (22%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 3 RVDGRLEELESRINEEARRLDRLHPLDAKHNVDVL-----EHDLRQAEENINTLFSDVQ 56
+D E+E+R+N ++D +N ++L + L + + N+N L++ V+
Sbjct: 65 IIDHEFSEIETRLNMINNKIDDQIQDIWTYNAELLVLLENQKTLDEHDANVNNLYNKVK 123
>3m5g_B Hemagglutinin; influenza virus, envelope protein, fusion Pro HOST
cell membrane, HOST membrane, membrane, transmembrane,
viral protein; HET: NAG; 2.60A {Influenza a virus} PDB:
3m5h_B* 3m5i_B* 3m5j_B*
Length = 182
Score = 23.8 bits (51), Expect = 6.2
Identities = 10/59 (16%), Positives = 23/59 (38%), Gaps = 5/59 (8%)
Query: 3 RVDGRLEELESRINEEARRLDRLHPLDAKHNVDVL-----EHDLRQAEENINTLFSDVQ 56
+D E+E +I +N ++L +H + A+ ++ L+ V+
Sbjct: 65 LIDNEFNEIEQQIGNVINWTRDAMTEIWSYNAELLVAMENQHTIDLADSEMSKLYERVK 123
>3ku3_B Hemagglutinin HA2 chain; viral envelope protein, viral fusion
protein, protein, viral protein; HET: NAG; 1.60A
{Influenza a virus} PDB: 3ku5_B* 3ku6_B* 3qqb_B* 3qqe_B*
3qqo_B* 3s11_B* 3s12_B* 3s13_B* 1jsm_B* 1jsn_B* 1jso_B*
2fk0_B* 3fku_B* 3gbm_B* 2ibx_B* 1rd8_B* 3gbn_B* 3lzf_B*
3r2x_B* 3sm5_B* ...
Length = 174
Score = 23.5 bits (50), Expect = 7.1
Identities = 11/59 (18%), Positives = 23/59 (38%), Gaps = 5/59 (8%)
Query: 3 RVDGRLEELESRINEEARRLDRLHPLDAKHNVDVL-----EHDLRQAEENINTLFSDVQ 56
V LE R+ ++++ +N ++L E L + N+ L+ V+
Sbjct: 65 AVGKEFSNLERRLENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVR 123
>2viu_B Hemagglutinin; envelope protein, glycoprotein; HET: NAG BMA; 2.50A
{Unidentified influenza virus} SCOP: h.3.1.1 PDB:
1eo8_B* 1hgd_B* 1hgf_B* 1hgg_B* 1hgh_B* 1hgi_B* 1hgj_B*
1ken_B* 1qfu_B* 2hmg_B* 1hge_B* 3hmg_B* 3ztj_B* 4hmg_B*
5hmg_B* 3sdy_B* 3eym_B* 3eyk_B* 3eyj_B* 1ti8_B* ...
Length = 175
Score = 23.5 bits (50), Expect = 8.0
Identities = 10/59 (16%), Positives = 26/59 (44%), Gaps = 5/59 (8%)
Query: 3 RVDGRLEELESRINEEARRLDRLHPLDAKHNVDVL-----EHDLRQAEENINTLFSDVQ 56
+++ E+E RI + + ++ +N ++L +H + + +N LF +
Sbjct: 65 QIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTR 123
>3tfo_A Putative 3-oxoacyl-(acyl-carrier-protein) reducta; structural
genomics, PSI-biology, NEW YORK structural genomi
research consortium; 2.08A {Sinorhizobium meliloti}
Length = 264
Score = 23.3 bits (51), Expect = 9.2
Identities = 7/33 (21%), Positives = 10/33 (30%), Gaps = 5/33 (15%)
Query: 19 ARRLDRLHPL-----DAKHNVDVLEHDLRQAEE 46
ARR R+ + DA D+
Sbjct: 35 ARRQARIEAIATEIRDAGGTALAQVLDVTDRHS 67
>1zud_1 Adenylyltransferase THIF; thiamin, thiazole, protein-protein
complex, THIF, TRAN biosynthetic protein complex; 1.98A
{Escherichia coli} PDB: 1zfn_A* 1zkm_A
Length = 251
Score = 23.2 bits (51), Expect = 9.5
Identities = 6/37 (16%), Positives = 14/37 (37%), Gaps = 5/37 (13%)
Query: 19 ARRLDRLHPLDAKHNVDVLEHDLRQAEENINTLFSDV 55
+RL +L+P ++ + R E + +
Sbjct: 88 QQRLTQLNP-----DIQLTALQQRLTGEALKDAVARA 119
>2yut_A Putative short-chain oxidoreductase; alpha and beta proteins
(A/B), NAD(P)-binding rossmann-fold structural
genomics, NPPSFA; HET: NAP; 2.20A {Thermus
thermophilus}
Length = 207
Score = 23.3 bits (51), Expect = 9.9
Identities = 7/27 (25%), Positives = 8/27 (29%)
Query: 19 ARRLDRLHPLDAKHNVDVLEHDLRQAE 45
RR L L + L DL
Sbjct: 29 GRRAGALAELAREVGARALPADLADEL 55
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
0.318 0.136 0.378
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,140,654
Number of extensions: 57658
Number of successful extensions: 284
Number of sequences better than 10.0: 1
Number of HSP's gapped: 283
Number of HSP's successfully gapped: 62
Length of query: 72
Length of database: 6,701,793
Length adjustment: 42
Effective length of query: 30
Effective length of database: 5,529,111
Effective search space: 165873330
Effective search space used: 165873330
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (23.4 bits)