RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy149
(86 letters)
>3flo_A DNA polymerase alpha subunit B; protein-protein complex,
phosphoesterase fold, OB fold, zinc-binding motif, DNA
replication; HET: DNA; 2.50A {Saccharomyces cerevisiae}
Length = 460
Score = 61.7 bits (149), Expect = 4e-13
Identities = 26/86 (30%), Positives = 48/86 (55%), Gaps = 10/86 (11%)
Query: 6 RSLSMFVSAGPYTQSDTLSYKPLEDLIA-LTVQQEPDVLILIGPLLDTSHPLLLNGSL-- 62
SL + V+ GPY +D S + L++ I + + +P VLI+ GP +D +HPL+ +G L
Sbjct: 146 SSLKVIVTCGPYFANDNFSLELLQEFIDSINNEVKPHVLIMFGPFIDITHPLIASGKLPN 205
Query: 63 -------AETFEDFYVKLIDSIVQPL 81
+T ++ ++KL I++ +
Sbjct: 206 FPQFKTQPKTLDELFLKLFTPILKTI 231
>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 = 34.6 bits (79), Expect = 0.002
Identities = 17/78 (21%), Positives = 28/78 (35%), Gaps = 12/78 (15%)
Query: 13 SAGPYT----QSDTLSYKPLEDLIALTVQQEPDVLILIGPLLDTSHPLLLN-GSLAETFE 67
+A Q +T Y E+L L L+G L+ S L E
Sbjct: 153 NAQLVAIFGGQGNTDDY--FEELRDLYQTYHV----LVGDLIKFSAETLSELIRTTLDAE 206
Query: 68 DFYVKLIDSIVQPLEKPG 85
+ + ++ I++ LE P
Sbjct: 207 KVFTQGLN-ILEWLENPS 223
>3tyg_A Envelope glycoprotein GP160; GP120, HIV-1, ENV, FAB, HIV-1
neutralizing antibody, immune viral protein; HET: NAG
BMA MAN; 3.25A {Human immunodeficiency virus 1}
Length = 199
Score = 28.9 bits (65), Expect = 0.13
Identities = 9/17 (52%), Positives = 10/17 (58%), Gaps = 5/17 (29%)
Query: 53 SHP-----LLLNGSLAE 64
+ LLLNGSLAE
Sbjct: 54 AGTVVSTQLLLNGSLAE 70
>2ny1_A Envelope glycoprotein GP120; HIV, GP120, CD4, viral protein-immune
system compl; HET: NAG SUC; 1.99A {Human
immunodeficiency virus 1} SCOP: d.172.1.1 PDB: 2nxz_A*
2nxy_A* 1g9m_G* 1rzj_G* 2ny7_G* 2ny5_G* 3idx_G* 3idy_G*
2ny2_A* 1gc1_G* 2ny4_A* 2ny3_A* 2ny6_A* 2ny0_A* 1yym_G*
1rzk_G* 1g9n_G* 1yyl_G* 2i5y_G* 2i60_G* ...
Length = 317
Score = 29.1 bits (66), Expect = 0.15
Identities = 19/46 (41%), Positives = 20/46 (43%), Gaps = 18/46 (39%)
Query: 56 LLLNGSLAE--------TFEDFYVKLIDSIVQ---PLE----KPGH 86
LLLNGSLAE F D K I IVQ +E GH
Sbjct: 113 LLLNGSLAEEEVVIRSVNFTD-NAKTI--IVQLNTSVEINCTGAGH 155
>3jwd_A HIV-1 GP120 envelope glycoprotein; HIV-1 viral spike, molecular
motion, protein architecture, R triggered entry, type 1
fusion protein, cell membrane, DISU bond; HET: YCM NAG;
2.61A {Human immunodeficiency virus 1} PDB: 1meq_A
Length = 379
Score = 28.7 bits (65), Expect = 0.16
Identities = 19/55 (34%), Positives = 23/55 (41%), Gaps = 18/55 (32%)
Query: 46 IGPLLDTSHPLLLNGSLAET-----FEDFY--VKLIDSIVQPLEK-------PGH 86
I P++ + LLLNGSLAE +F K I IVQ GH
Sbjct: 148 IRPVVSSQ--LLLNGSLAEEEVVIRSVNFTDNAKTI--IVQLNTSVEINCTGAGH 198
>4dkp_A Clade A/E 93TH057 HIV-1 GP120 core; CD4 mimic, AWS-I-50, viral
protein-I complex; HET: NAG EPE 0LL; 1.80A {Human
immunodeficiency virus type 1} PDB: 4dko_A* 4dkq_A*
4dkr_A* 3se8_G* 3ngb_G* 3se9_G* 3tgt_A* 3u7y_G* 3rjq_A*
3tgs_A* 3tgr_A* 3tih_A 3tgq_A* 3jwo_A* 2qad_A* 3hi1_G*
3dnl_B 3dnn_B 3dno_B 3dnl_C ...
Length = 353
Score = 28.7 bits (65), Expect = 0.17
Identities = 9/9 (100%), Positives = 9/9 (100%)
Query: 56 LLLNGSLAE 64
LLLNGSLAE
Sbjct: 143 LLLNGSLAE 151
>2bf1_A SIV GP120, exterior membrane glycoprotein GP120; virus protein,
envelope glycoprotein, AIDS, coat protein; HET: NAG BMA
NDG FUC MAN; 4.0A {Simian immunodeficiency virus} PDB:
3fus_A*
Length = 316
Score = 28.3 bits (64), Expect = 0.24
Identities = 4/9 (44%), Positives = 5/9 (55%)
Query: 56 LLLNGSLAE 64
NG+ AE
Sbjct: 115 FGFNGTRAE 123
>2ohw_A YUEI protein; structural genomics, PSI-2, protein structure
initiative, NEW YORK SGX research center for structural
genomics, nysgxrc; 1.40A {Bacillus subtilis} SCOP:
d.79.8.1
Length = 133
Score = 27.4 bits (61), Expect = 0.41
Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 4/47 (8%)
Query: 31 LIALTVQQ--EPDVLILIGPLLDTSHP--LLLNGSLAETFEDFYVKL 73
++ALT Q L SH LL+NG L Y+++
Sbjct: 38 VLALTKGQVLRSKPYKEAEHELKNSHNVTLLINGELQYQSYSSYIQM 84
>1ii7_A MRE11 nuclease; RAD50, DNA double-strand break repair, DAMP,
manganese, replication; HET: DA; 2.20A {Pyrococcus
furiosus} SCOP: d.159.1.4 PDB: 3dsc_A* 3dsd_A* 1s8e_A
Length = 333
Score = 25.5 bits (56), Expect = 2.5
Identities = 7/28 (25%), Positives = 16/28 (57%)
Query: 28 LEDLIALTVQQEPDVLILIGPLLDTSHP 55
++ + + VQ+ D +++ G L +S P
Sbjct: 29 FKNALEIAVQENVDFILIAGDLFHSSRP 56
>3av0_A DNA double-strand break repair protein MRE11; DNA repair,
calcineurin-like phosphoesterase, ABC transporte
domain-like; HET: DNA AGS; 3.10A {Methanocaldococcus
jannaschii} PDB: 3auz_A*
Length = 386
Score = 25.2 bits (55), Expect = 3.0
Identities = 8/31 (25%), Positives = 15/31 (48%)
Query: 25 YKPLEDLIALTVQQEPDVLILIGPLLDTSHP 55
Y + I ++ +PDV++ G L + P
Sbjct: 46 YDSFKLCIKKILEIKPDVVLHSGDLFNDLRP 76
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 0.137 0.386
Gapped
Lambda K H
0.267 0.0815 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,202,655
Number of extensions: 58971
Number of successful extensions: 156
Number of sequences better than 10.0: 1
Number of HSP's gapped: 154
Number of HSP's successfully gapped: 16
Length of query: 86
Length of database: 6,701,793
Length adjustment: 54
Effective length of query: 32
Effective length of database: 5,194,059
Effective search space: 166209888
Effective search space used: 166209888
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 (23.3 bits)