BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 028804
(203 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1VCS|A Chain A, Solution Structure Of Rsgi Ruh-009, An N-Terminal Domain
Of Vti1a [mus Musculus]
Length = 102
Score = 54.7 bits (130), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 51/89 (57%), Gaps = 2/89 (2%)
Query: 8 YERQYCELSAGLSRKCTAASALDGELKKQKLSEIKTGLDDADALIRKMDLEARSLQPNVK 67
YE+ + L+A ++ K L + KKQ ++ ++ L++A L+ +MDLE R + P +
Sbjct: 10 YEQDFAVLTAEITSKIARVPRLPPDEKKQMVANVEKQLEEARELLEQMDLEVREIPPQSR 69
Query: 68 AMLLSKLREYKTDLNNLKNEVK--RVTSG 94
M +++R YK ++ L+ + K R+ SG
Sbjct: 70 GMYSNRMRSYKQEMGKLETDFKRSRIASG 98
>pdb|2NPS|C Chain C, Crystal Structure Of The Early Endosomal Snare Complex
Length = 81
Score = 30.4 bits (67), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 30/49 (61%)
Query: 120 RGRLLMSTERLNHSTDRIKESRRTMLETEELGVSILQDLHQQRQSLLHA 168
R LL +TERL S+ R++ + +ETE++G +L++L R+ + A
Sbjct: 4 RAHLLDNTERLERSSRRLEAGYQIAVETEQIGQEMLENLSHDRERIQRA 52
>pdb|3LW6|A Chain A, Crystal Structure Of Drosophila
Beta1,4-Galactosyltransferas
Length = 287
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 34/71 (47%)
Query: 30 DGELKKQKLSEIKTGLDDADALIRKMDLEARSLQPNVKAMLLSKLREYKTDLNNLKNEVK 89
D L+ + IKTG +D + I R Q +++ R++KT L+N+K ++
Sbjct: 196 DAGLQVTRPQNIKTGTNDTFSHIHNRYHRKRDTQKCFNQKEMTRKRDHKTGLDNVKYKIL 255
Query: 90 RVTSGNVNQAA 100
+V ++Q
Sbjct: 256 KVHEMLIDQVP 266
>pdb|1GL2|C Chain C, Crystal Structure Of An Endosomal Snare Core Complex
Length = 65
Score = 28.9 bits (63), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 23/36 (63%)
Query: 130 LNHSTDRIKESRRTMLETEELGVSILQDLHQQRQSL 165
+N +T I+ S R ET+++G I+++L +QR L
Sbjct: 4 MNRATQSIERSHRIATETDQIGTEIIEELGEQRDQL 39
>pdb|2PKP|A Chain A, Crystal Structure Of 3-Isopropylmalate Dehydratase (Leud)
From Methhanocaldococcus Jannaschii Dsm2661 (Mj1271)
Length = 170
Score = 28.1 bits (61), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 19/33 (57%)
Query: 13 CELSAGLSRKCTAASALDGELKKQKLSEIKTGL 45
CE GL R+ AA L LKK+KL + K G+
Sbjct: 136 CETPKGLEREILAAGGLVNYLKKRKLIQSKKGV 168
>pdb|3E0D|A Chain A, Insights Into The Replisome From The Crystral Structure Of
The Ternary Complex Of The Eubacterial Dna Polymerase
Iii Alpha-Subunit
pdb|3E0D|B Chain B, Insights Into The Replisome From The Crystral Structure Of
The Ternary Complex Of The Eubacterial Dna Polymerase
Iii Alpha-Subunit
Length = 1220
Score = 28.1 bits (61), Expect = 3.5, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 4/71 (5%)
Query: 75 REYKTDLNNLKNEVKRVTSGNVNQAARDELLESGMADAMMVSADQRGRLLMSTERLNHST 134
RE +L + +KR+ VN+ A + L+++G DA R RLL S E L
Sbjct: 909 RERGGPFKSLGDFLKRLPEQVVNKRALESLVKAGALDAF----GDRARLLASLEPLLRWA 964
Query: 135 DRIKESRRTML 145
+E R+ L
Sbjct: 965 AETRERGRSGL 975
>pdb|2HPI|A Chain A, Eubacterial And Eukaryotic Replicative Dna Polymerases Are
Not Homologous: X-Ray Structure Of Dna Polymerase Iii
pdb|2HPM|A Chain A, Eubacterial And Eukaryotic Replicative Dna Polymerases Are
Not Homologous: X-ray Structure Of Dna Polymerase Iii
Length = 1220
Score = 28.1 bits (61), Expect = 3.5, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 4/71 (5%)
Query: 75 REYKTDLNNLKNEVKRVTSGNVNQAARDELLESGMADAMMVSADQRGRLLMSTERLNHST 134
RE +L + +KR+ VN+ A + L+++G DA R RLL S E L
Sbjct: 909 RERGGPFKSLGDFLKRLPEQVVNKRALESLVKAGALDAF----GDRARLLASLEPLLRWA 964
Query: 135 DRIKESRRTML 145
+E R+ L
Sbjct: 965 AETRERGRSGL 975
>pdb|2V71|A Chain A, Coiled-Coil Region Of Nudel
pdb|2V71|B Chain B, Coiled-Coil Region Of Nudel
Length = 189
Score = 27.7 bits (60), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 9/69 (13%)
Query: 98 QAARDELLE--------SGMADAMMVSADQRGRLLMS-TERLNHSTDRIKESRRTMLETE 148
Q ARDEL+E +A +V A+QR R L + +RL + + +KE
Sbjct: 27 QEARDELVEFQEGSRELEAELEAQLVQAEQRNRDLQADNQRLKYEVEALKEKLEHQYAQS 86
Query: 149 ELGVSILQD 157
VS+L+D
Sbjct: 87 YKQVSVLED 95
>pdb|2V8S|V Chain V, Vti1b Habc Domain - Epsinr Enth Domain Complex
Length = 96
Score = 27.7 bits (60), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 30/58 (51%)
Query: 32 ELKKQKLSEIKTGLDDADALIRKMDLEARSLQPNVKAMLLSKLREYKTDLNNLKNEVK 89
E KK+ + + +A+ + +M+ E R + ++SKLR Y+ DL L EV+
Sbjct: 39 EEKKKLVRDFDEKQQEANETLAEMEEELRYAPLTFRNPMMSKLRNYRKDLAKLHREVR 96
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.130 0.367
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,009,518
Number of Sequences: 62578
Number of extensions: 163885
Number of successful extensions: 530
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 519
Number of HSP's gapped (non-prelim): 25
length of query: 203
length of database: 14,973,337
effective HSP length: 94
effective length of query: 109
effective length of database: 9,091,005
effective search space: 990919545
effective search space used: 990919545
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)