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= 026949
(230 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 = 117 bits (292), Expect = 6e-27, Method: Compositional matrix adjust.
Identities = 75/219 (34%), Positives = 124/219 (56%), Gaps = 9/219 (4%)
Query: 6 VSKQIQQMVRFIRQEAEEKANEISVSAEEEFNIEKLQLVEAEKKKIRQEYERKEKQVEIR 65
V+ ++ +M FIR+EAEEKA EI + A++E+ IEK +V E I ++ K K+ +
Sbjct: 13 VNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKLKKAMLS 72
Query: 66 KKIEYSMQLNASRIKVLQAQDDLVSNMMEAASKEVLNVSRDHNSYKKLLKGLIVQSLLRL 125
++I S N R+KVL A++ + + E +++ ++ + + YK +L+ LIV++LL+L
Sbjct: 73 QQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPILQSLIVEALLKL 132
Query: 126 KEPAVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLXXXXXXXXXXXXS 185
EP +++ + D L+ES+ + EY +K Q P E IV + YL
Sbjct: 133 LEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLNKDL--------- 183
Query: 186 CSGGVVVASRDGKIVCENTLDARLDVVFRKKLPEIRKQL 224
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 = 42.0 bits (97), Expect = 3e-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 = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 31/133 (23%), Positives = 61/133 (45%), Gaps = 22/133 (16%)
Query: 78 RIKVLQAQDDLVSNMMEAASKEVLNVSRDHNSYKKLLKGLIVQSLLRLKEPAVLLRCRKD 137
R K L Q++++S+++E + + +S D Y + +K L+ +++ L E V + +
Sbjct: 72 RRKRLAIQEEIISSVLEEVKRRLETMSEDE--YFESVKALLKEAIKELNEKKVRVMSNEK 129
Query: 138 DHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLXXXXXXXXXXXXSCSGGVVVASRDG 197
L+ S +E K E + + E + GGV+V + DG
Sbjct: 130 TLGLIASRIEEIKSELGD-VSIELGETV-------------------DTMGGVIVETEDG 169
Query: 198 KIVCENTLDARLD 210
+I +NT +AR++
Sbjct: 170 RIRIDNTFEARME 182
>pdb|4DT0|A Chain A, The Structure Of The Peripheral Stalk Subunit E From
Pyrococcus Horikoshii
Length = 208
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 33/133 (24%), Positives = 60/133 (45%), Gaps = 22/133 (16%)
Query: 78 RIKVLQAQDDLVSNMMEAASKEVLNVSRDHNSYKKLLKGLIVQSLLRLKEPAVLLRCRKD 137
R K L Q++++S+++E + + +S D Y + +K L+ +++ L E V + +
Sbjct: 82 RRKRLAIQEEIISSVLEEVKRRLETMSEDE--YFESVKALLKEAIKELNEKKVRVMSNEK 139
Query: 138 DHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLXXXXXXXXXXXXSCSGGVVVASRDG 197
L+ S +E K E D I L GGV+V + DG
Sbjct: 140 TLGLIASRIEEIKSELG------------DVSIELGETV--------DTMGGVIVETEDG 179
Query: 198 KIVCENTLDARLD 210
+I +NT +AR++
Sbjct: 180 RIRIDNTFEARME 192
>pdb|2DMA|A Chain A, Crystal Structure Of Ph1978 From Pyrococcus Horikoshii Ot3
(Form Ii)
Length = 198
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 31/133 (23%), Positives = 59/133 (44%), Gaps = 22/133 (16%)
Query: 78 RIKVLQAQDDLVSNMMEAASKEVLNVSRDHNSYKKLLKGLIVQSLLRLKEPAVLLRCRKD 137
R K L Q++++S+++E + + S D Y + +K L+ +++ L E V + +
Sbjct: 72 RRKRLAIQEEIISSVLEEVKRRLETXSEDE--YFESVKALLKEAIKELNEKKVRVXSNEK 129
Query: 138 DHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLXXXXXXXXXXXXSCSGGVVVASRDG 197
L+ S +E K E + + E + GGV+V + DG
Sbjct: 130 TLGLIASRIEEIKSELGD-VSIELGETV-------------------DTXGGVIVETEDG 169
Query: 198 KIVCENTLDARLD 210
+I +NT +AR +
Sbjct: 170 RIRIDNTFEARXE 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 = 0.72, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 20/30 (66%)
Query: 190 VVVASRDGKIVCENTLDARLDVVFRKKLPE 219
V V ++ G +VC+N ++ +D++ K LP+
Sbjct: 46 VGVPTKSGNVVCKNIMNTGVDIICTKNLPK 75
>pdb|3QKT|A Chain A, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
Complex With Amp- Pnp
pdb|3QKT|B Chain B, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
Complex With Amp- Pnp
pdb|3QKT|C Chain C, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
Complex With Amp- Pnp
pdb|3QKT|D Chain D, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
Complex With Amp- Pnp
Length = 339
Score = 28.5 bits (62), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 31/56 (55%), Gaps = 7/56 (12%)
Query: 66 KKIEYSMQLNASRIKVLQAQDDLVSNMMEAASK---EVLNVSRDHNSYKKL--LKG 116
K I Y++ LNA I + Q Q D + EA K EVLN+ + +YKKL LKG
Sbjct: 125 KLIPYNIFLNA--IYIRQGQIDAILESDEAREKVVREVLNLDKFETAYKKLSELKG 178
>pdb|3QKU|A Chain A, Mre11 Rad50 Binding Domain In Complex With Rad50 And
Amp-Pnp
pdb|3QKU|B Chain B, Mre11 Rad50 Binding Domain In Complex With Rad50 And
Amp-Pnp
Length = 359
Score = 27.3 bits (59), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 5/51 (9%)
Query: 66 KKIEYSMQLNASRIKVLQAQDDLVSNMMEAASK---EVLNVSRDHNSYKKL 113
K I Y++ LNA I + Q Q D + EA K EVLN+ + +YKKL
Sbjct: 125 KLIPYNIFLNA--IYIRQGQIDAILESDEAREKVVREVLNLDKFETAYKKL 173
>pdb|3QKR|A Chain A, Mre11 Rad50 Binding Domain Bound To Rad50
pdb|3QKS|A Chain A, Mre11 Rad50 Binding Domain Bound To Rad50
Length = 203
Score = 26.9 bits (58), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 5/51 (9%)
Query: 66 KKIEYSMQLNASRIKVLQAQDDLVSNMMEAASK---EVLNVSRDHNSYKKL 113
K I Y++ LNA I + Q Q D + EA K EVLN+ + +YKKL
Sbjct: 125 KLIPYNIFLNA--IYIRQGQIDAILESDEAREKVVREVLNLDKFETAYKKL 173
>pdb|1II8|A Chain A, Crystal Structure Of The P. Furiosus Rad50 Atpase Domain
Length = 195
Score = 26.9 bits (58), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 5/51 (9%)
Query: 66 KKIEYSMQLNASRIKVLQAQDDLVSNMMEAASK---EVLNVSRDHNSYKKL 113
K I Y++ LNA I + Q Q D + EA K EVLN+ + +YKKL
Sbjct: 125 KLIPYNIFLNA--IYIRQGQIDAILESDEAREKVVREVLNLDKFETAYKKL 173
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
0.315 0.130 0.340
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,335,738
Number of Sequences: 62578
Number of extensions: 170934
Number of successful extensions: 762
Number of sequences better than 100.0: 46
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 36
Number of HSP's that attempted gapping in prelim test: 738
Number of HSP's gapped (non-prelim): 53
length of query: 230
length of database: 14,973,337
effective HSP length: 96
effective length of query: 134
effective length of database: 8,965,849
effective search space: 1201423766
effective search space used: 1201423766
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: 50 (23.9 bits)