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= 032198
(145 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 = 69.7 bits (169), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 42/82 (51%), Positives = 54/82 (65%)
Query: 60 VPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPGLGSAGGGTTAKDAIGNDIIAADW 119
VPDMG+RQ MNLL G V+ L P +F PP G AGGGTTAKD +GND+ + +
Sbjct: 10 VPDMGRRQFMNLLTFGTVTGVALGALYPVVNYFIPPAAGGAGGGTTAKDELGNDVSVSKF 69
Query: 120 LNTHGPGDRTLTEGLKQDFSHL 141
L +H GDRTL +GLK D +++
Sbjct: 70 LESHNVGDRTLVQGLKGDPTYI 91
>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 = 66.2 bits (160), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 39/82 (47%), Positives = 53/82 (64%)
Query: 60 VPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPGLGSAGGGTTAKDAIGNDIIAADW 119
VPDMG+RQ MNLL G V+ L P +F PP G+ GGGTTAKD +GN++ + +
Sbjct: 10 VPDMGRRQFMNLLAFGTVTGVALGALYPLVKYFIPPSGGAVGGGTTAKDKLGNNVKVSKF 69
Query: 120 LNTHGPGDRTLTEGLKQDFSHL 141
L +H GDR L +GLK D +++
Sbjct: 70 LESHNAGDRVLVQGLKGDPTYI 91
>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 = 66.2 bits (160), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 39/82 (47%), Positives = 53/82 (64%)
Query: 60 VPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPGLGSAGGGTTAKDAIGNDIIAADW 119
VPDMG+RQ MNLL G V+ L P +F PP G+ GGGTTAKD +GN++ + +
Sbjct: 10 VPDMGRRQFMNLLAFGTVTGVALGALYPLVKYFIPPSGGAVGGGTTAKDKLGNNVKVSKF 69
Query: 120 LNTHGPGDRTLTEGLKQDFSHL 141
L +H GDR L +GLK D +++
Sbjct: 70 LESHNAGDRVLVQGLKGDPTYI 91
>pdb|1RFS|A Chain A, Rieske Soluble Fragment From Spinach
Length = 139
Score = 63.2 bits (152), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 34/50 (68%), Positives = 41/50 (82%)
Query: 92 FAPPGLGSAGGGTTAKDAIGNDIIAADWLNTHGPGDRTLTEGLKQDFSHL 141
F PPG G+ GGT AKDA+GND+IAA+WL TH PGDRTLT+GLK D ++L
Sbjct: 1 FVPPGGGAGTGGTIAKDALGNDVIAAEWLKTHAPGDRTLTQGLKGDPTYL 50
>pdb|1Q90|C Chain C, Structure Of The Cytochrome B6f (Plastohydroquinone :
Plastocyanin Oxidoreductase) From Chlamydomonas
Reinhardtii
Length = 127
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/36 (61%), Positives = 29/36 (80%)
Query: 106 AKDAIGNDIIAADWLNTHGPGDRTLTEGLKQDFSHL 141
AKDA+GNDI A +WL TH GDR+L++GLK D ++L
Sbjct: 3 AKDALGNDIKAGEWLKTHLAGDRSLSQGLKGDPTYL 38
>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 = 42.7 bits (99), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 19/40 (47%), Positives = 29/40 (72%)
Query: 102 GGTTAKDAIGNDIIAADWLNTHGPGDRTLTEGLKQDFSHL 141
G AKDA+GNDI +++L H PGDR+L +G+K D +++
Sbjct: 5 GRAVAKDALGNDIKVSEYLAKHLPGDRSLAQGIKGDPTYV 44
>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|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 = 10/30 (33%), Positives = 20/30 (66%)
Query: 61 PDMGKRQLMNLLLLGAVSLPTGFMLVPYAT 90
P+MG + + N + +GA++ G ++P+AT
Sbjct: 288 PEMGHKGITNFIRIGALAAEHGIDVIPHAT 317
>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 = 1.5, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 20/30 (66%)
Query: 61 PDMGKRQLMNLLLLGAVSLPTGFMLVPYAT 90
P+MG + + N + +GA++ G ++P+AT
Sbjct: 308 PEMGHKGITNFIRIGALAAEHGIDVIPHAT 337
>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 = 26.2 bits (56), Expect = 7.5, Method: Composition-based stats.
Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 95 PGLGSAGGGTTAKDAIGN---DIIAADWLNTHGPGDRTLTEGLKQDFSHL 141
P + +G G KD G D ++ WLN HG + L + +K+ +
Sbjct: 27 PLIIESGTGIKVKDINGKEYYDGFSSVWLNVHGHRKKELDDAIKKQLGKI 76
>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 = 26.2 bits (56), Expect = 7.7, Method: Composition-based stats.
Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 95 PGLGSAGGGTTAKDAIGN---DIIAADWLNTHGPGDRTLTEGLKQDFSHL 141
P + +G G KD G D ++ WLN HG + L + +K+ +
Sbjct: 27 PLIIESGTGIKVKDINGKEYYDGFSSVWLNVHGHRKKELDDAIKKQLGKI 76
>pdb|3LNP|A Chain A, Crystal Structure Of Amidohydrolase Family Protein
Olei01672_1_465 From Oleispira Antarctica
Length = 468
Score = 25.8 bits (55), Expect = 9.7, Method: Composition-based stats.
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 110 IGNDIIAADWLNTHGPGDRTLTEGLKQDF 138
+G ++ W+N HG +L GL D
Sbjct: 79 LGQQVLXPGWVNAHGHAAXSLFRGLADDL 107
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
0.322 0.138 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,983,153
Number of Sequences: 62578
Number of extensions: 156035
Number of successful extensions: 278
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 267
Number of HSP's gapped (non-prelim): 13
length of query: 145
length of database: 14,973,337
effective HSP length: 89
effective length of query: 56
effective length of database: 9,403,895
effective search space: 526618120
effective search space used: 526618120
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)