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= 028203
(212 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4DL0|J Chain J, Crystal Structure Of The Heterotrimeric Egchead Peripheral
Stalk Complex Of The Yeast Vacuolar Atpase
pdb|4DL0|E Chain E, Crystal Structure Of The Heterotrimeric Egchead Peripheral
Stalk Complex Of The Yeast Vacuolar Atpase
pdb|4EFA|E Chain E, Crystal Structure Of The Heterotrimeric Egchead Peripheral
Stalk Complex Of The Yeast Vacuolar Atpase - Second
Conformation
Length = 233
Score = 93.2 bits (230), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 72/219 (32%), Positives = 111/219 (50%), Gaps = 27/219 (12%)
Query: 6 VSKQIQQMVRFIRQEAEEKANEISVSAEEEFNIEKLQLVEAEKKKIRQEYERKEKQVEIR 65
V+ ++ +M FIR+EAEEKA EI + A++E+ IEK +V E I ++ K K+ +
Sbjct: 13 VNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKLKKAMLS 72
Query: 66 KKIEYSMQLNASRIKVLQAQDDLVSNMMEAAS-------------KEVLNS-----LLRL 107
++I S N R+KVL A++ + + E K +L S LL+L
Sbjct: 73 QQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPILQSLIVEALLKL 132
Query: 108 KEPAVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLXXXXXXXXXXXXS 167
EP +++ + D L+ES+ + EY +K Q P E IV + YL
Sbjct: 133 LEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLNKDL--------- 183
Query: 168 CSGGVVVASRDGKIVCENTLDARLDVVFRKKLPEIRKQL 206
SGGVVV++ KI NTL+ RL ++ + LP IR +L
Sbjct: 184 VSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLEL 222
>pdb|2KZ9|A Chain A, Structure Of E1-69 Of Yeast V-Atpase
Length = 69
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 36/57 (63%)
Query: 6 VSKQIQQMVRFIRQEAEEKANEISVSAEEEFNIEKLQLVEAEKKKIRQEYERKEKQV 62
V+ ++ +M FIR+EAEEKA EI + A++E+ IEK +V E I ++ K K+
Sbjct: 13 VNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKLKKA 69
>pdb|2DM9|A Chain A, Crystal Structure Of Ph1978 From Pyrococcus Horikoshii Ot3
pdb|2DM9|B Chain B, Crystal Structure Of Ph1978 From Pyrococcus Horikoshii Ot3
Length = 198
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 11/23 (47%), Positives = 18/23 (78%)
Query: 170 GGVVVASRDGKIVCENTLDARLD 192
GGV+V + DG+I +NT +AR++
Sbjct: 160 GGVIVETEDGRIRIDNTFEARME 182
>pdb|4DT0|A Chain A, The Structure Of The Peripheral Stalk Subunit E From
Pyrococcus Horikoshii
Length = 208
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 11/23 (47%), Positives = 18/23 (78%)
Query: 170 GGVVVASRDGKIVCENTLDARLD 192
GGV+V + DG+I +NT +AR++
Sbjct: 170 GGVIVETEDGRIRIDNTFEARME 192
>pdb|2DMA|A Chain A, Crystal Structure Of Ph1978 From Pyrococcus Horikoshii Ot3
(Form Ii)
Length = 198
Score = 31.6 bits (70), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 168 CSGGVVVASRDGKIVCENTLDARLD 192
GGV+V + DG+I +NT +AR +
Sbjct: 158 TXGGVIVETEDGRIRIDNTFEARXE 182
>pdb|2JOV|A Chain A, Nmr Structure Of Clostridium Perfringens Protein Cpe0013.
Northeast Structural Genomics Target Cpr31
Length = 85
Score = 30.8 bits (68), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 20/30 (66%)
Query: 172 VVVASRDGKIVCENTLDARLDVVFRKKLPE 201
V V ++ G +VC+N ++ +D++ K LP+
Sbjct: 46 VGVPTKSGNVVCKNIMNTGVDIICTKNLPK 75
>pdb|2WYH|A Chain A, Structure Of The Streptococcus Pyogenes Family Gh38 Alpha-
Mannosidase
pdb|2WYH|B Chain B, Structure Of The Streptococcus Pyogenes Family Gh38 Alpha-
Mannosidase
pdb|2WYI|A Chain A, Structure Of The Streptococcus Pyogenes Family Gh38 Alpha-
Mannosidase Complexed With Swainsonine
pdb|2WYI|B Chain B, Structure Of The Streptococcus Pyogenes Family Gh38 Alpha-
Mannosidase Complexed With Swainsonine
Length = 923
Score = 28.5 bits (62), Expect = 3.0, Method: Composition-based stats.
Identities = 24/105 (22%), Positives = 47/105 (44%), Gaps = 19/105 (18%)
Query: 28 ISVSAEEEFNIEKLQLVEAEKKKIRQEYERKEKQVEIRKKIEYSMQLNASRIKVLQAQDD 87
I +SA++ E +++ +++ R R +++ E+ M+ N R++ D+
Sbjct: 636 IPISADKLLQAEMEAVIDITERQAR----RSQEKAELTLTTLIRMEKNNPRLQFTTRFDN 691
Query: 88 LVSNMMEAASKEVLNSLLRLKEPAVLLRCRKDDHHLVESVLESAK 132
++ N LR+ P L K DHHL +S+ E+ K
Sbjct: 692 -----------QMTNHRLRVLFPTHL----KTDHHLADSIFETVK 721
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
0.314 0.129 0.337
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,863,669
Number of Sequences: 62578
Number of extensions: 153361
Number of successful extensions: 702
Number of sequences better than 100.0: 37
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 27
Number of HSP's that attempted gapping in prelim test: 682
Number of HSP's gapped (non-prelim): 45
length of query: 212
length of database: 14,973,337
effective HSP length: 95
effective length of query: 117
effective length of database: 9,028,427
effective search space: 1056325959
effective search space used: 1056325959
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)