RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16695
(101 letters)
>3cue_A Transport protein particle 23 kDa subunit; membrane traffic, GEF,
tethering complex, RAB activation, GU nucleotide
exchange factor; HET: PLM; 3.70A {Saccharomyces
cerevisiae}
Length = 219
Score = 81.6 bits (200), Expect = 1e-20
Identities = 23/64 (35%), Positives = 36/64 (56%)
Query: 37 APTNYQRSGSNEPGRNLASSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQN 96
+ + NLA D L+K+Y LY+DY +K+P YS+EMPIR LFD ++
Sbjct: 154 TIATTDKPDRPKSTSNLAIQIADNFLRKVYCLYSDYVMKDPSYSMEMPIRSNLFDEKVKK 213
Query: 97 LLQQ 100
+++
Sbjct: 214 MVEN 217
>2j3t_D Trafficking protein particle complex subunit 4; trapp, palmitate,
transport, lipoprotein, ER-golgi transport apparatus,
protein transport; HET: PLM; 2.4A {Homo sapiens} PDB:
2zmv_A 2jsn_A
Length = 219
Score = 79.4 bits (195), Expect = 5e-20
Identities = 30/47 (63%), Positives = 40/47 (85%)
Query: 55 SSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQH 101
+G+D +L+KIYE+Y+D+ALKNPFYSLEMPIRCELFD +L+ L+
Sbjct: 163 QAGIDSLLRKIYEIYSDFALKNPFYSLEMPIRCELFDQNLKLALEVA 209
>2j3t_C Trafficking protein particle complex subunit 1, trafficking protein
particle complex subunit 3; trapp, palmitate, transport,
lipoprotein, ER-golgi transport apparatus, protein
transport; HET: PLM; 2.4A {Mus musculus}
Length = 145
Score = 71.4 bits (175), Expect = 1e-17
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 55 SSGLDLILKKIYE-LYADYALKNPFYSLEMPIRCELFDTHLQNLLQQ 100
+ +L IY LY ++ +KNP L ++ ELF + L + ++
Sbjct: 90 VGPIRDVLHHIYSALYVEFVVKNPLCPLGQTVQSELFRSRLDSYVRS 136
>2j3w_A Sedlin, trafficking protein particle complex protein 2;
multisubunit tethering factor, trapp, palmitate,
transport, lipoprotein; HET: PLM; 2.1A {Mus musculus}
SCOP: d.110.4.3 PDB: 1h3q_A
Length = 142
Score = 60.4 bits (146), Expect = 2e-13
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 56 SGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQH 101
G+ +Y+LY +A+ NPFY PIR FD +Q L ++H
Sbjct: 95 DGIKNFFTDVYDLYIKFAM-NPFYEPNSPIRSSAFDRKVQFLGKKH 139
>3cue_C Transport protein particle 18 kDa subunit; membrane traffic, GEF,
tethering complex, RAB activation, GU nucleotide
exchange factor; HET: PLM; 3.70A {Saccharomyces
cerevisiae}
Length = 159
Score = 54.5 bits (131), Expect = 6e-11
Identities = 10/62 (16%), Positives = 18/62 (29%), Gaps = 14/62 (22%)
Query: 52 NLASSGLDLILKKIY-ELYADYALKNPFYSLEMP-------------IRCELFDTHLQNL 97
+ +L+ IY +Y Y N + I F + L++
Sbjct: 93 DFKQQSYTQVLQYIYSHIYVKYVSNNLLSPYDFAENENEMRGQGTRKITNRNFISVLESF 152
Query: 98 LQ 99
L
Sbjct: 153 LA 154
>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 = 27.7 bits (61), Expect = 0.66
Identities = 14/117 (11%), Positives = 28/117 (23%), Gaps = 36/117 (30%)
Query: 11 LRWNEYHP-VDNTHLIQQQEQHRHIDVAPTNYQ-RSGSNEPGRNLASSGL---------D 59
L N+ H + ++ R + P ++S L
Sbjct: 96 LEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQ 155
Query: 60 LI---------------LKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQH 101
L+ L+ +Y+ Y L + L L++
Sbjct: 156 LVAIFGGQGNTDDYFEELRDLYQTYH--VLVGDL--------IKFSAETLSELIRTT 202
Score = 25.8 bits (56), Expect = 2.8
Identities = 7/43 (16%), Positives = 15/43 (34%), Gaps = 5/43 (11%)
Query: 28 QEQHRHIDVAPTNYQRS---GSNEPGRNLASSGLDL--ILKKI 65
E + + + P+ + S P L+ S L + +
Sbjct: 311 YEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYV 353
>3jqo_A TRAF protein; helical outer membrane TM, outer membrane protein
complex, plasmid, transport protein; HET: LDA; 2.60A
{Escherichia coli}
Length = 227
Score = 27.3 bits (60), Expect = 0.72
Identities = 8/50 (16%), Positives = 19/50 (38%), Gaps = 4/50 (8%)
Query: 20 DNTHLIQQQEQHRHIDVAPTNYQRSGSNEPGRNLASSGLDLILKKIYELY 69
++ + + ++ + PT Y + G + + DL +Y L
Sbjct: 180 NSGGQLASEALRSYMSIPPTLYDQQG--DAVSIFVAR--DLDFSGVYTLA 225
>1n13_B PVLARGDC, pyruvoyl-dependent arginine decarboxylase alpha chain;
pyruvoyl group, pyruvate, agmatine, lyase; 1.40A
{Methanocaldococcus jannaschii} SCOP: d.155.1.2 PDB:
1mt1_B 2qqd_B 2qqc_B
Length = 113
Score = 26.3 bits (58), Expect = 1.3
Identities = 6/19 (31%), Positives = 11/19 (57%)
Query: 38 PTNYQRSGSNEPGRNLASS 56
PT Y S+ PG ++++
Sbjct: 22 PTAYGYIISDVPGETISAA 40
>3iwf_A Transcription regulator RPIR family; transcriptional, N-terminal,
PSI, MCSG, structural genomics, midwest center
structural genomics; 1.40A {Staphylococcus epidermidis}
Length = 107
Score = 24.2 bits (53), Expect = 6.8
Identities = 9/35 (25%), Positives = 11/35 (31%), Gaps = 10/35 (28%)
Query: 61 ILKKIYELY----------ADYALKNPFYSLEMPI 85
IL KI Y A + L P + M
Sbjct: 4 ILYKIDNQYPYFTKNEKKIAQFILNYPHKVVNMTS 38
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
0.319 0.135 0.432
Gapped
Lambda K H
0.267 0.0654 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,587,986
Number of extensions: 78282
Number of successful extensions: 121
Number of sequences better than 10.0: 1
Number of HSP's gapped: 119
Number of HSP's successfully gapped: 13
Length of query: 101
Length of database: 6,701,793
Length adjustment: 67
Effective length of query: 34
Effective length of database: 4,831,086
Effective search space: 164256924
Effective search space used: 164256924
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 (21.8 bits)
S2: 51 (23.6 bits)