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= 031683
(155 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZT9|D Chain D, Crystal Structure Of The Cytochrome B6f Complex From
Nostoc Sp. Pcc 7120
pdb|4H44|D Chain D, 2.70 A Cytochrome B6f Complex Structure From Nostoc Pcc
7120
Length = 179
Score = 68.2 bits (165), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 41/76 (53%), Positives = 50/76 (65%)
Query: 60 VPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPGLGSAGGGTTAKDAIGNDIIAADW 119
VPDMG+RQ MNLL G V+ L P +F PP G AGGGTTAKD +GND+ + +
Sbjct: 10 VPDMGRRQFMNLLTFGTVTGVALGALYPVVNYFIPPAAGGAGGGTTAKDELGNDVSVSKF 69
Query: 120 LNTHGPGDRTLTEGLK 135
L +H GDRTL +GLK
Sbjct: 70 LESHNVGDRTLVQGLK 85
>pdb|2E74|D Chain D, Crystal Structure Of The Cytochrome B6f Complex From
M.Laminosus
pdb|2E75|D Chain D, Crystal Structure Of The Cytochrome B6f Complex With
2-nonyl-4- Hydroxyquinoline N-oxide (nqno) From
M.laminosus
pdb|2E76|D Chain D, Crystal Structure Of The Cytochrome B6f Complex With
Tridecyl- Stigmatellin (Tds) From M.Laminosus
pdb|4H0L|D Chain D, Cytochrome B6f Complex Crystal Structure From
Mastigocladus Laminosus With N-side Inhibitor Nqno
pdb|4H13|D Chain D, Crystal Structure Of The Cytochrome B6f Complex From
Mastigocladus Laminosus With Tds
Length = 179
Score = 64.7 bits (156), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 38/76 (50%), Positives = 49/76 (64%)
Query: 60 VPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPGLGSAGGGTTAKDAIGNDIIAADW 119
VPDMG+RQ MNLL G V+ L P +F PP G+ GGGTTAKD +GN++ + +
Sbjct: 10 VPDMGRRQFMNLLAFGTVTGVALGALYPLVKYFIPPSGGAVGGGTTAKDKLGNNVKVSKF 69
Query: 120 LNTHGPGDRTLTEGLK 135
L +H GDR L +GLK
Sbjct: 70 LESHNAGDRVLVQGLK 85
>pdb|1VF5|D Chain D, Crystal Structure Of Cytochrome B6f Complex From
M.Laminosus
pdb|1VF5|Q Chain Q, Crystal Structure Of Cytochrome B6f Complex From
M.Laminosus
pdb|2D2C|D Chain D, Crystal Structure Of Cytochrome B6f Complex With Dbmib
From M. Laminosus
pdb|2D2C|Q Chain Q, Crystal Structure Of Cytochrome B6f Complex With Dbmib
From M. Laminosus
Length = 179
Score = 64.7 bits (156), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 38/76 (50%), Positives = 49/76 (64%)
Query: 60 VPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPGLGSAGGGTTAKDAIGNDIIAADW 119
VPDMG+RQ MNLL G V+ L P +F PP G+ GGGTTAKD +GN++ + +
Sbjct: 10 VPDMGRRQFMNLLAFGTVTGVALGALYPLVKYFIPPSGGAVGGGTTAKDKLGNNVKVSKF 69
Query: 120 LNTHGPGDRTLTEGLK 135
L +H GDR L +GLK
Sbjct: 70 LESHNAGDRVLVQGLK 85
>pdb|1RFS|A Chain A, Rieske Soluble Fragment From Spinach
Length = 139
Score = 60.1 bits (144), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 32/44 (72%), Positives = 37/44 (84%)
Query: 92 FAPPGLGSAGGGTTAKDAIGNDIIAADWLNTHGPGDRTLTEGLK 135
F PPG G+ GGT AKDA+GND+IAA+WL TH PGDRTLT+GLK
Sbjct: 1 FVPPGGGAGTGGTIAKDALGNDVIAAEWLKTHAPGDRTLTQGLK 44
>pdb|1Q90|C Chain C, Structure Of The Cytochrome B6f (Plastohydroquinone :
Plastocyanin Oxidoreductase) From Chlamydomonas
Reinhardtii
Length = 127
Score = 46.2 bits (108), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 20/30 (66%), Positives = 25/30 (83%)
Query: 106 AKDAIGNDIIAADWLNTHGPGDRTLTEGLK 135
AKDA+GNDI A +WL TH GDR+L++GLK
Sbjct: 3 AKDALGNDIKAGEWLKTHLAGDRSLSQGLK 32
>pdb|1Q90|R Chain R, Structure Of The Cytochrome B6f (Plastohydroquinone :
Plastocyanin Oxidoreductase) From Chlamydomonas
Reinhardtii
Length = 49
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/39 (46%), Positives = 23/39 (58%)
Query: 57 ADRVPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAPP 95
+ VPDM KR +MNL+L G LP + + Y FF PP
Sbjct: 3 SSEVPDMNKRNIMNLILAGGAGLPITTLALGYGAFFVPP 41
>pdb|3AZC|A Chain A, Crystal Structure Of The Soluble Part Of Cytochrome B6f
Complex Iron- Sulfur Subunit From Thermosynechococcus
Elongatus Bp-1
Length = 133
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/34 (52%), Positives = 25/34 (73%)
Query: 102 GGTTAKDAIGNDIIAADWLNTHGPGDRTLTEGLK 135
G AKDA+GNDI +++L H PGDR+L +G+K
Sbjct: 5 GRAVAKDALGNDIKVSEYLAKHLPGDRSLAQGIK 38
>pdb|4DN1|A Chain A, Crystal Structure Of An Enolase (Mandelate Racemase
Subgroup Member) From Agrobacterium Tumefaciens (Target
Efi-502088) With Bound Mg And Formate
pdb|4DN1|B Chain B, Crystal Structure Of An Enolase (Mandelate Racemase
Subgroup Member) From Agrobacterium Tumefaciens (Target
Efi-502088) With Bound Mg And Formate
Length = 408
Score = 28.5 bits (62), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 61 PDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFA 93
P+MG + + N + +GA++ G ++P+AT A
Sbjct: 308 PEMGHKGITNFIRIGALAAEHGIDVIPHATVGA 340
>pdb|2NQL|A Chain A, Crystal Structure Of A Member Of The Enolase Superfamily
From Agrobacterium Tumefaciens
pdb|2NQL|B Chain B, Crystal Structure Of A Member Of The Enolase Superfamily
From Agrobacterium Tumefaciens
Length = 388
Score = 28.5 bits (62), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 61 PDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFA 93
P+MG + + N + +GA++ G ++P+AT A
Sbjct: 288 PEMGHKGITNFIRIGALAAEHGIDVIPHATVGA 320
>pdb|3DOD|A Chain A, Crystal Structure Of Plp Bound 7,8-diaminopelargonic Acid
Synthase In Bacillus Subtilis
pdb|3DOD|B Chain B, Crystal Structure Of Plp Bound 7,8-diaminopelargonic Acid
Synthase In Bacillus Subtilis
pdb|3DRD|A Chain A, Crystal Structure Of 7,8 Diaminopelargonic Acid Synthase
Apoenzyme In Bacillus Subtilis
pdb|3DRD|B Chain B, Crystal Structure Of 7,8 Diaminopelargonic Acid Synthase
Apoenzyme In Bacillus Subtilis
Length = 448
Score = 28.1 bits (61), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 95 PGLGSAGGGTTAKDAIGN---DIIAADWLNTHGPGDRTLTEGLKVQI 138
P + +G G KD G D ++ WLN HG + L + +K Q+
Sbjct: 27 PLIIESGTGIKVKDINGKEYYDGFSSVWLNVHGHRKKELDDAIKKQL 73
>pdb|3DU4|A Chain A, Crystal Structure Of 7-Keto-8-Aminopelargonic Acid Bound
7,8- Diaminopelargonic Acid Synthase In Bacillus
Subtilis
pdb|3DU4|B Chain B, Crystal Structure Of 7-Keto-8-Aminopelargonic Acid Bound
7,8- Diaminopelargonic Acid Synthase In Bacillus
Subtilis
Length = 448
Score = 28.1 bits (61), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 95 PGLGSAGGGTTAKDAIGN---DIIAADWLNTHGPGDRTLTEGLKVQI 138
P + +G G KD G D ++ WLN HG + L + +K Q+
Sbjct: 27 PLIIESGTGIKVKDINGKEYYDGFSSVWLNVHGHRKKELDDAIKKQL 73
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 27.3 bits (59), Expect = 3.1, Method: Composition-based stats.
Identities = 22/90 (24%), Positives = 37/90 (41%), Gaps = 11/90 (12%)
Query: 67 QLMNLLLLGAVSLPTGFMLVPYATFF--------APPGLGSAGGGTTAKDAIGNDIIAAD 118
+L+N + + +PT +++ Y TF GL G K++ +A
Sbjct: 157 KLVNFISQQGMRIPTPILIISYETFRLHAEVLHKGKVGLVICDEGHRLKNSDNQTYLA-- 214
Query: 119 WLNTHGPGDRTLTEGLKVQINFFENYCLVH 148
LN+ R L G +Q + E + LVH
Sbjct: 215 -LNSMNAQRRVLISGTPIQNDLLEYFSLVH 243
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
0.323 0.139 0.443
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,367,245
Number of Sequences: 62578
Number of extensions: 176082
Number of successful extensions: 308
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 298
Number of HSP's gapped (non-prelim): 12
length of query: 155
length of database: 14,973,337
effective HSP length: 91
effective length of query: 64
effective length of database: 9,278,739
effective search space: 593839296
effective search space used: 593839296
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 47 (22.7 bits)