RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6927
(93 letters)
>3fbi_A Mediator of RNA polymerase II transcription subunit 7;
proline-rich stretches, right-handed four-helix bundle,
protein-protein complex; 2.80A {Saccharomyces
cerevisiae} PDB: 3fbn_A
Length = 84
Score = 28.4 bits (63), Expect = 0.13
Identities = 8/48 (16%), Positives = 16/48 (33%)
Query: 42 PPLRWKTFVANRVSKIQELVSEDKWFHVKGTENPADCLSRGITPKELI 89
PP K F + + K+ + + + N ++ S L
Sbjct: 17 PPPYVKFFTQSNLEKLPKYKEKKAASAKQTAPNNSNGGSEEEITCALD 64
>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 = 28.3 bits (62), Expect = 0.35
Identities = 6/40 (15%), Positives = 13/40 (32%), Gaps = 16/40 (40%)
Query: 5 CGKTFLILEHSLNSIQAFSWVTYRDGDSQVAL----YWIS 40
GKT++ L+ Q + +W++
Sbjct: 161 SGKTWVALD------------VCLSYKVQCKMDFKIFWLN 188
>2kse_A Sensor protein QSEC; methods development, histidine kinase
receptor, membrane domain, two-helical hairpin,
cell-free synthesis, ATP- binding; NMR {Escherichia
coli}
Length = 186
Score = 26.6 bits (58), Expect = 0.95
Identities = 6/42 (14%), Positives = 15/42 (35%)
Query: 22 FSWVTYRDGDSQVALYWISSPPLRWKTFVANRVSKIQELVSE 63
F+ D W++SP +++ V +++
Sbjct: 118 FADGQLVGEDDPWRFVWMTSPDGKYRIVVGQEWEYREDMALA 159
>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 = 25.4 bits (55), Expect = 3.9
Identities = 15/77 (19%), Positives = 24/77 (31%), Gaps = 21/77 (27%)
Query: 22 FSWVTYRDGDSQVA---LYWISSPPLRWKTFVANR-----------VSKIQELVSEDK-- 65
F R ++ + I P++W+T + S + L +K
Sbjct: 463 FDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDG 522
Query: 66 -WFHV--KGT--ENPAD 77
V GT NP D
Sbjct: 523 TGVRVIVAGTLDINPDD 539
>4a5s_A Dipeptidyl peptidase 4 soluble form; hydrolase, type 2 diabetes,
novartis compound NVP-BIV988; HET: N7F NAG MAN; 1.62A
{Homo sapiens} PDB: 2qjr_A* 3f8s_A* 2qt9_A* 2qtb_A*
2rip_A* 1tk3_A* 1n1m_A* 1nu8_A* 1rwq_A* 1nu6_A* 1tkr_A*
1w1i_A* 2ajl_I* 2bgn_A* 2bub_A* 2ogz_A* 2ole_A* 2oqi_A*
3bjm_A* 3eio_A* ...
Length = 740
Score = 25.2 bits (55), Expect = 4.0
Identities = 8/61 (13%), Positives = 22/61 (36%)
Query: 14 HSLNSIQAFSWVTYRDGDSQVALYWISSPPLRWKTFVANRVSKIQELVSEDKWFHVKGTE 73
+L+ + ++ +G + + I + T V I+ L S+ ++ +
Sbjct: 326 FTLDGNSFYKIISNEEGYRHICYFQIDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYK 385
Query: 74 N 74
Sbjct: 386 G 386
>3dc8_A Dihydropyrimidinase; TIM-barrel, hydrolase; HET: KCX; 1.85A
{Sinorhizobium meliloti}
Length = 490
Score = 24.9 bits (55), Expect = 4.5
Identities = 8/19 (42%), Positives = 9/19 (47%)
Query: 27 YRDGDSQVALYWISSPPLR 45
Y D D A + SPP R
Sbjct: 272 YFDKDWDHAARRVMSPPFR 290
>3hlz_A Uncharacterized protein BT_1490; NP_810393.1, structural genomics,
joint center for structural genomics, JCSG; HET: MSE;
1.50A {Bacteroides thetaiotaomicron vpi-5482}
Length = 269
Score = 25.0 bits (54), Expect = 4.8
Identities = 7/31 (22%), Positives = 13/31 (41%), Gaps = 7/31 (22%)
Query: 17 NSIQAFSWVTYRDGDSQVALYWISSPPLRWK 47
N ++ W T DG+ + P L ++
Sbjct: 213 NEVEGMEWKTLIDGNRE-------VPVLEYQ 236
>2vr2_A Dihydropyrimidinase; hydantoinase, metal-binding, disease mutation,
dihydropyrimi amidohydrolase, nucleotide metabolism,
DPYS, dhpase, hydrolase; 2.80A {Homo sapiens}
Length = 541
Score = 25.0 bits (55), Expect = 5.1
Identities = 6/19 (31%), Positives = 10/19 (52%)
Query: 27 YRDGDSQVALYWISSPPLR 45
Y + + A + + PPLR
Sbjct: 306 YWNKEWHHAAHHVMGPPLR 324
>2iv2_X Formate dehydrogenase H; oxidoreductase, 4Fe-4S, anaerobic,
complete proteome, direct protein sequencing, Fe4S4,
iron, iron sulfur cluster; HET: 2MD MGD; 2.27A
{Escherichia coli} SCOP: b.52.2.2 c.81.1.1 PDB: 1fdi_A*
1fdo_A* 1aa6_A*
Length = 715
Score = 24.4 bits (54), Expect = 6.4
Identities = 7/37 (18%), Positives = 13/37 (35%), Gaps = 4/37 (10%)
Query: 53 RVSKIQELVSEDKWFHVKGTENPADCLSRGITPKELI 89
+ + L E + + N D GI + L+
Sbjct: 594 NCAALAALADEPGYAQI----NTEDAKRLGIEDEALV 626
>2xhi_A N-glycosylase/DNA lyase; lyase-DNA complex, lyase/DNA complex,
separation-OF-function helix-hairpin-helix, DNA repair;
HET: 8OG; 1.55A {Homo sapiens} PDB: 1ko9_A 1lwy_A*
1hu0_A* 1lwv_A* 1lww_A* 2noe_A* 2noh_A* 2nol_A* 1n3c_A*
1fn7_A* 2noz_A* 1yqk_A 1yqr_A* 1yql_A* 1yqm_A* 2noi_A
1ebm_A* 1m3q_A* 1m3h_A* 1n39_A* ...
Length = 360
Score = 24.3 bits (52), Expect = 8.9
Identities = 8/27 (29%), Positives = 12/27 (44%)
Query: 4 RCGKTFLILEHSLNSIQAFSWVTYRDG 30
C ++ L L+ L S Q+F W
Sbjct: 42 PCPRSELRLDLVLPSGQSFRWREQSPA 68
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
0.320 0.133 0.426
Gapped
Lambda K H
0.267 0.0620 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,380,966
Number of extensions: 62393
Number of successful extensions: 150
Number of sequences better than 10.0: 1
Number of HSP's gapped: 150
Number of HSP's successfully gapped: 13
Length of query: 93
Length of database: 6,701,793
Length adjustment: 60
Effective length of query: 33
Effective length of database: 5,026,533
Effective search space: 165875589
Effective search space used: 165875589
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (23.7 bits)