RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy416
(157 letters)
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 32.1 bits (72), Expect = 0.050
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 12/47 (25%)
Query: 91 PVSMAQWDEE----LEERAAQEYKIMLLDALEARWR--AETESACYY 131
P S+ +W EE L+E A +E WR A+ + +
Sbjct: 84 PESIRKWREEQRKRLQELDAASKV------MEQEWREKAKKDLEEWN 124
>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 = 31.2 bits (70), Expect = 0.13
Identities = 17/92 (18%), Positives = 36/92 (39%), Gaps = 21/92 (22%)
Query: 26 LSVALLQGAVEL-ENLP---LKKDALRQLGIPIEIKSGFIGKVKLQVPVSQFRSAPWVIC 81
L ++L+ ++E E +P L ++ + E ++ K +P + +
Sbjct: 319 LPPSILEDSLENNEGVPSPML---SIS--NLTQEQVQDYVNKTNSHLPAGK------QVE 367
Query: 82 I-----EQLYVVTG-PVSMAQWDEELEERAAQ 107
I + VV+G P S+ + L + A
Sbjct: 368 ISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAP 399
Score = 28.1 bits (62), Expect = 1.4
Identities = 30/165 (18%), Positives = 56/165 (33%), Gaps = 57/165 (34%)
Query: 17 YVENL----NTDQLSVA-LLQGAVE-LENL---PLKKDALRQLGIPIEIKSGFIGKVKLQ 67
Y E L T + V L++ + E L L L + + G+ I + L+
Sbjct: 169 YFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNIL---EW-----LE 220
Query: 68 VPVSQFRSAPWVICIEQLYVVTGPVSM-----AQWDEELEERAAQEYKIML--LD----A 116
P + P ++ Y+++ P+S Q A Y + L
Sbjct: 221 NPSN----TP-----DKDYLLSIPISCPLIGVIQ--------LAH-YVVTAKLLGFTPGE 262
Query: 117 LEARWRAETE------SACYYSSSYTSWLSYGTSFMTNIVENLQV 155
L + + T +A + + SW SF ++ + + V
Sbjct: 263 LRSYLKGATGHSQGLVTAVAIAET-DSW----ESFFVSVRKAITV 302
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 30.2 bits (68), Expect = 0.32
Identities = 14/57 (24%), Positives = 19/57 (33%), Gaps = 27/57 (47%)
Query: 108 EYKIMLLDALEARWRAETESACYYSSSYTSWLSY------------GTSFM--TNIV 150
E K+ L + L RW +E SW + GT M NI+
Sbjct: 642 ESKLSL-ETLFNRWHSE------------SWANQLTVCGAIIGWTRGTGLMSANNII 685
>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 = 29.4 bits (65), Expect = 0.54
Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 10/52 (19%)
Query: 3 ERLIAWVLNNYLGKYVENL----NTDQLSVALLQGAVELENLPLKKDALRQL 50
ERL+ + ++L K ENL TD LL+ A+ E+ + ++A +Q+
Sbjct: 542 ERLVN-AILDFLPKIEENLICSKYTD-----LLRIALMAEDEAIFEEAHKQV 587
>2o0b_A 3-phosphoshikimate 1-carboxyvinyltransferase; shikimate pathway,
EPSP synthase, structural genomics; HET: S3P; 1.15A
{Mycobacterium tuberculosis} PDB: 2o0d_A* 2o0e_A*
2o0x_A* 2o0z_A* 2o15_A 2bjb_A
Length = 450
Score = 28.7 bits (65), Expect = 0.70
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 11/43 (25%)
Query: 45 DALRQLGIPIE--------IKSGFI--GKVKLQVPVS-QFRSA 76
DALR+LG+ ++ +G + G V + S QF S
Sbjct: 131 DALRELGVAVDGTGLPFRVRGNGSLAGGTVAIDASASSQFVSG 173
Score = 26.4 bits (59), Expect = 5.3
Identities = 9/36 (25%), Positives = 17/36 (47%), Gaps = 6/36 (16%)
Query: 26 LSVALLQGAVELENLPLKKD------ALRQLGIPIE 55
L+ A +GA + +D AL+ LG+ ++
Sbjct: 35 LAAAQGRGASTISGALRSRDTELMLDALQTLGLRVD 70
>3iz5_S 60S ribosomal protein L18A (L18AE); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_S 3izc_S 3izs_S
Length = 178
Score = 27.8 bits (61), Expect = 1.7
Identities = 9/71 (12%), Positives = 16/71 (22%), Gaps = 2/71 (2%)
Query: 2 LERLIAWVLNNYLGKYVENLNTDQLSVALLQGAVELENLPLKKDALRQLGIPIEIKSGFI 61
L V Y + + V + K+D +Q
Sbjct: 98 DTTLNGAVEQMYTEMASRHRVRFPCIQIIKTATVHFK--LCKRDNTKQFHKSDIKFPLVY 155
Query: 62 GKVKLQVPVSQ 72
KV+ +
Sbjct: 156 RKVRPPTRKLK 166
>3nvs_A 3-phosphoshikimate 1-carboxyvinyltransferase; structural genomics,
center for structural genomics of infec diseases, csgid;
HET: S3P SKM GPJ EPE; 1.02A {Vibrio cholerae} PDB:
1g6s_A* 1g6t_A* 1x8r_A* 1x8t_A* 2aa9_A* 2aay_A* 2pq9_A*
1eps_A 1mi4_A* 3fjz_A* 3fjx_A* 2qfs_A* 2qft_A* 2qfq_A*
2qfu_A* 3fk0_A* 3fk1_A* 1q36_A* 3ti2_A* 1p88_A ...
Length = 450
Score = 27.6 bits (62), Expect = 1.9
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 14/46 (30%)
Query: 45 DALRQLGI-----------PIEIKSGFI--GKVKLQVPVS-QFRSA 76
DALRQ G P+ I+ + G V + +S QF +A
Sbjct: 155 DALRQAGAQIEYLEQENFPPLRIQGTGLQAGTVTIDGSISSQFLTA 200
Score = 26.4 bits (59), Expect = 4.8
Identities = 26/114 (22%), Positives = 39/114 (34%), Gaps = 34/114 (29%)
Query: 29 ALLQGAVELENLPLKKD------ALRQLGIPIEIKS--------GFIGKVKLQVPVSQF- 73
AL G L NL D AL +LG+ + + G P+ F
Sbjct: 57 ALASGTTRLTNLLDSDDIRHMLNALTKLGVNYRLSADKTTCEVEGLGQAFHTTQPLELFL 116
Query: 74 -------RSAPWVICI-EQLYVVTGPVSMAQWDEELEERAAQEYKIMLLDALEA 119
R +C+ + YV+TG + ++ER L+DAL
Sbjct: 117 GNAGTAMRPLAAALCLGQGDYVLTG-------EPRMKERPIGH----LVDALRQ 159
>3u5i_q A0, L10E, 60S acidic ribosomal protein P0; translation, ribosome,
ribosomal R ribosomal protein, STM1; 3.00A
{Saccharomyces cerevisiae} PDB: 3izc_s 3izs_s 3j16_G*
3o5h_M 3jyw_8
Length = 312
Score = 26.2 bits (57), Expect = 4.7
Identities = 13/70 (18%), Positives = 24/70 (34%), Gaps = 2/70 (2%)
Query: 2 LERLIAWVLNNYLGKYVENLNTDQLSVALLQGAVELENLPLKKDALRQLGIPIEIKSGFI 61
L + +++N + + + +E P K + LG+P +I G I
Sbjct: 93 LTEIKNVIVSNRVAAPARAGAVAPEDIWVRAVNTGME--PGKTSFFQALGVPTKIARGTI 150
Query: 62 GKVKLQVPVS 71
V V
Sbjct: 151 EIVSDVKVVD 160
>1rf6_A 5-enolpyruvylshikimate-3-phosphate synthase; shikimate pathway,
EPSP synthase, glyphosate, PEP, transferase; HET: GPJ
S3P; 1.90A {Streptococcus pneumoniae} SCOP: d.68.2.2
PDB: 1rf5_A 1rf4_A*
Length = 427
Score = 26.0 bits (58), Expect = 7.3
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 6/39 (15%)
Query: 29 ALLQGAVELENLPLKKD------ALRQLGIPIEIKSGFI 61
+L +G ++ ++ +D R LG+ IE K G I
Sbjct: 31 SLAEGETKVYDILRGEDVLSTMQVFRDLGVEIEDKDGVI 69
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
0.317 0.132 0.389
Gapped
Lambda K H
0.267 0.0510 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,445,239
Number of extensions: 135911
Number of successful extensions: 397
Number of sequences better than 10.0: 1
Number of HSP's gapped: 394
Number of HSP's successfully gapped: 22
Length of query: 157
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 71
Effective length of database: 4,300,587
Effective search space: 305341677
Effective search space used: 305341677
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: 53 (24.7 bits)