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= psy1109
(79 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1OCC|G Chain G, Structure Of Bovine Heart Cytochrome C Oxidase At The
Fully Oxidized State
pdb|1OCC|T Chain T, Structure Of Bovine Heart Cytochrome C Oxidase At The
Fully Oxidized State
pdb|2OCC|G Chain G, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State
pdb|2OCC|T Chain T, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State
pdb|1OCO|G Chain G, Bovine Heart Cytochrome C Oxidase In Carbon
Monoxide-bound State
pdb|1OCO|T Chain T, Bovine Heart Cytochrome C Oxidase In Carbon
Monoxide-bound State
pdb|1OCR|G Chain G, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
State
pdb|1OCR|T Chain T, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
State
pdb|1OCZ|G Chain G, Bovine Heart Cytochrome C Oxidase In Azide-Bound State
pdb|1OCZ|T Chain T, Bovine Heart Cytochrome C Oxidase In Azide-Bound State
pdb|2YBB|R Chain R, Fitted Model For Bovine Mitochondrial Supercomplex
I1iii2iv1 By Single Particle Cryo-Em (Emd-1876)
Length = 84
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 29/61 (47%), Gaps = 5/61 (8%)
Query: 18 AMKSSAGNPDAVKLWRNLTYFGALPCCALVGVYVYLEHQAEEEHHVRPEFVKREYLYIRN 77
A K G A + WR LT+ ALP AL + +L H E RP F+ +L IR
Sbjct: 3 AAKGDHGGTGA-RTWRFLTFGLALPSVALCTLNSWL-HSGHRE---RPAFIPYHHLRIRT 57
Query: 78 R 78
+
Sbjct: 58 K 58
>pdb|2Y69|G Chain G, Bovine Heart Cytochrome C Oxidase Re-Refined With
Molecular Oxygen
pdb|2Y69|T Chain T, Bovine Heart Cytochrome C Oxidase Re-Refined With
Molecular Oxygen
Length = 97
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 29/61 (47%), Gaps = 5/61 (8%)
Query: 18 AMKSSAGNPDAVKLWRNLTYFGALPCCALVGVYVYLEHQAEEEHHVRPEFVKREYLYIRN 77
A K G A + WR LT+ ALP AL + +L H E RP F+ +L IR
Sbjct: 15 AAKGDHGGXGA-RTWRFLTFGLALPSVALCTLNSWL-HSGHRE---RPAFIPYHHLRIRT 69
Query: 78 R 78
+
Sbjct: 70 K 70
>pdb|1V54|G Chain G, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State
pdb|1V54|T Chain T, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State
pdb|1V55|G Chain G, Bovine Heart Cytochrome C Oxidase At The Fully Reduced
State
pdb|1V55|T Chain T, Bovine Heart Cytochrome C Oxidase At The Fully Reduced
State
pdb|2DYR|G Chain G, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State
pdb|2DYR|T Chain T, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State
pdb|2DYS|G Chain G, Bovine Heart Cytochrome C Oxidase Modified By Dccd
pdb|2DYS|T Chain T, Bovine Heart Cytochrome C Oxidase Modified By Dccd
pdb|2EIJ|G Chain G, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
State
pdb|2EIJ|T Chain T, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
State
pdb|2EIK|G Chain G, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome
C Oxidase In The Fully Reduced State
pdb|2EIK|T Chain T, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome
C Oxidase In The Fully Reduced State
pdb|2EIL|G Chain G, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome
C Oxidase In The Fully Oxidized State
pdb|2EIL|T Chain T, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome
C Oxidase In The Fully Oxidized State
pdb|2EIM|G Chain G, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
Oxidase In The Fully Reduced State
pdb|2EIM|T Chain T, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
Oxidase In The Fully Reduced State
pdb|2EIN|G Chain G, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
Oxidase In The Fully Oxidized State
pdb|2EIN|T Chain T, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
Oxidase In The Fully Oxidized State
pdb|2ZXW|G Chain G, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State (1-S X-Ray Exposure Dataset)
pdb|2ZXW|T Chain T, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State (1-S X-Ray Exposure Dataset)
pdb|3ABL|G Chain G, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State (15-S X-Ray Exposure Dataset)
pdb|3ABL|T Chain T, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State (15-S X-Ray Exposure Dataset)
pdb|3ABM|G Chain G, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State (200-S X-Ray Exposure Dataset)
pdb|3ABM|T Chain T, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State (200-S X-Ray Exposure Dataset)
pdb|3ABK|G Chain G, Bovine Heart Cytochrome C Oxidase At The No-Bound Fully
Reduced State (50k)
pdb|3ABK|T Chain T, Bovine Heart Cytochrome C Oxidase At The No-Bound Fully
Reduced State (50k)
pdb|3AG1|G Chain G, Bovine Heart Cytochrome C Oxidase In The Carbon
Monoxide-Bou Reduced State At 280 K
pdb|3AG1|T Chain T, Bovine Heart Cytochrome C Oxidase In The Carbon
Monoxide-Bou Reduced State At 280 K
pdb|3AG2|G Chain G, Bovine Heart Cytochrome C Oxidase In The Carbon
Monoxide-Bou Reduced State At 100 K
pdb|3AG2|T Chain T, Bovine Heart Cytochrome C Oxidase In The Carbon
Monoxide-Bou Reduced State At 100 K
pdb|3AG3|G Chain G, Bovine Heart Cytochrome C Oxidase In The Nitric
Oxide-Bound Reduced State At 100 K
pdb|3AG3|T Chain T, Bovine Heart Cytochrome C Oxidase In The Nitric
Oxide-Bound Reduced State At 100 K
pdb|3AG4|G Chain G, Bovine Heart Cytochrome C Oxidase In The Cyanide
Ion-Bound F Reduced State At 100 K
pdb|3AG4|T Chain T, Bovine Heart Cytochrome C Oxidase In The Cyanide
Ion-Bound F Reduced State At 100 K
pdb|3ASN|G Chain G, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
State Measured At 1.7470 Angstrom Wavelength
pdb|3ASN|T Chain T, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
State Measured At 1.7470 Angstrom Wavelength
pdb|3ASO|G Chain G, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
State Measured At 0.9 Angstrom Wavelength
pdb|3ASO|T Chain T, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
State Measured At 0.9 Angstrom Wavelength
Length = 85
Score = 30.4 bits (67), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 29/61 (47%), Gaps = 5/61 (8%)
Query: 18 AMKSSAGNPDAVKLWRNLTYFGALPCCALVGVYVYLEHQAEEEHHVRPEFVKREYLYIRN 77
A K G A + WR LT+ ALP AL + +L H E RP F+ +L IR
Sbjct: 3 AAKGDHGGXGA-RTWRFLTFGLALPSVALCTLNSWL-HSGHRE---RPAFIPYHHLRIRT 57
Query: 78 R 78
+
Sbjct: 58 K 58
>pdb|1G5F|A Chain A, Structure Of Linb Complexed With 1,2-Dichloroethane
pdb|1G4H|A Chain A, Linb Complexed With Butan-1-Ol
pdb|1G42|A Chain A, Structure Of 1,3,4,6-Tetrachloro-1,4-Cyclohexadiene
Hydrolase (Linb) From Sphingomonas Paucimobilis
Complexed With 1,2-Dichloropropane
Length = 296
Score = 26.2 bits (56), Expect = 4.8, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 17/50 (34%)
Query: 24 GNPDAVKLWRNL----TYFGALPCCALVGV-------------YVYLEHQ 56
GNP + LWRN+ G L C L+G+ Y Y EH+
Sbjct: 37 GNPTSSYLWRNIMPHCAGLGRLIACDLIGMGDSDKLDPSGPERYAYAEHR 86
>pdb|1IZ7|A Chain A, Re-Refinement Of The Structure Of Hydrolytic Haloalkane
Dehalogenase Linb From Sphingomonas Paucimobilis Ut26
At 1.6 A Resolution
pdb|1IZ8|A Chain A, Re-Refinement Of The Structure Of Hydrolytic Haloalkane
Dehalogenase Linb From Sphingomonas Paucimobilis Ut26
With 1,3-Propanediol, A Product Of Debromidation Of
Dibrompropane, At 2.0a Resolution
pdb|1K5P|A Chain A, Hydrolytic Haloalkane Dehalogenase Linb From
Sphingomonas Paucimobilis Ut26 At 1.8a Resolution
pdb|1K63|A Chain A, Complex Of Hydrolytic Haloalkane Dehalogenase Linb From
Sphingomonas Paucimobilis With Ut26
2-Bromo-2-Propene-1-Ol At 1.8a Resolution
pdb|1K6E|A Chain A, Complex Of Hydrolytic Haloalkane Dehalogenase Linb From
Sphingomonas Paucimobilis Ut26 With 1,2-Propanediol
(Product Of Dehalogenation Of 1,2-Dibromopropane) At
1.85a
Length = 295
Score = 26.2 bits (56), Expect = 5.0, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 17/50 (34%)
Query: 24 GNPDAVKLWRNL----TYFGALPCCALVGV-------------YVYLEHQ 56
GNP + LWRN+ G L C L+G+ Y Y EH+
Sbjct: 36 GNPTSSYLWRNIMPHCAGLGRLIACDLIGMGDSDKLDPSGPERYAYAEHR 85
>pdb|1MJ5|A Chain A, Linb (Haloalkane Dehalogenase) From Sphingomonas
Paucimobilis Ut26 At Atomic Resolution
Length = 302
Score = 26.2 bits (56), Expect = 5.1, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 17/50 (34%)
Query: 24 GNPDAVKLWRNL----TYFGALPCCALVGV-------------YVYLEHQ 56
GNP + LWRN+ G L C L+G+ Y Y EH+
Sbjct: 37 GNPTSSYLWRNIMPHCAGLGRLIACDLIGMGDSDKLDPSGPERYAYAEHR 86
>pdb|1CV2|A Chain A, Hydrolytic Haloalkane Dehalogenase Linb From
Sphingomonas Paucimobilis Ut26 At 1.6 A Resolution
pdb|1D07|A Chain A, Hydrolytic Haloalkane Dehalogenase Linb From
Sphingomonas Paucimobilis Ut26 With 1,3-Propanediol, A
Product Of Debromidation Of Dibrompropane, At 2.0a
Resolution
pdb|2BFN|A Chain A, The Crystal Structure Of The Complex Of The Haloalkane
Dehalogenase Linb With The Product Of Dehalogenation
Reaction 1,2-Dichloropropane
Length = 296
Score = 26.2 bits (56), Expect = 5.1, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 17/50 (34%)
Query: 24 GNPDAVKLWRNL----TYFGALPCCALVGV-------------YVYLEHQ 56
GNP + LWRN+ G L C L+G+ Y Y EH+
Sbjct: 37 GNPTSSYLWRNIMPHCAGLGRLIACDLIGMGDSDKLDPSGPERYAYAEHR 86
>pdb|2QVB|A Chain A, Crystal Structure Of Haloalkane Dehalogenase Rv2579 From
Mycobacterium Tuberculosis
pdb|2QVB|B Chain B, Crystal Structure Of Haloalkane Dehalogenase Rv2579 From
Mycobacterium Tuberculosis
Length = 297
Score = 25.8 bits (55), Expect = 6.0, Method: Composition-based stats.
Identities = 13/30 (43%), Positives = 16/30 (53%), Gaps = 4/30 (13%)
Query: 24 GNPDAVKLWRN----LTYFGALPCCALVGV 49
GNP + LWRN L G L C L+G+
Sbjct: 36 GNPTSSYLWRNIMPHLEGLGRLVACDLIGM 65
>pdb|2O2H|A Chain A, Crystal Structure Of Haloalkane Dehalogenase Rv2579 From
Mycobacterium Tuberculosis Complexed With
1,2-Dichloroethane
pdb|2O2I|A Chain A, Crystal Structure Of Haloalkane Dehalogenase Rv2579 From
Mycobacterium Tuberculosis Complexed With
1,3-Propandiol
Length = 300
Score = 25.8 bits (55), Expect = 6.0, Method: Composition-based stats.
Identities = 13/30 (43%), Positives = 16/30 (53%), Gaps = 4/30 (13%)
Query: 24 GNPDAVKLWRN----LTYFGALPCCALVGV 49
GNP + LWRN L G L C L+G+
Sbjct: 38 GNPTSSYLWRNIMPHLEGLGRLVACDLIGM 67
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 0.134 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,340,668
Number of Sequences: 62578
Number of extensions: 77133
Number of successful extensions: 171
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 170
Number of HSP's gapped (non-prelim): 10
length of query: 79
length of database: 14,973,337
effective HSP length: 48
effective length of query: 31
effective length of database: 11,969,593
effective search space: 371057383
effective search space used: 371057383
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)