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= 040420
(169 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|6RXN|A Chain A, The Structure Of Rubredoxin From Desulfovibrio
Desulfuricans
Length = 46
Score = 50.4 bits (119), Expect = 4e-07, Method: Composition-based stats.
Identities = 22/43 (51%), Positives = 28/43 (65%), Gaps = 4/43 (9%)
Query: 77 QAYICRDCGYIYN----ERKPFDQLPDNYFCPVCGAPKRRFRP 115
Q Y+C CGY Y+ + PFDQLPD++ CPVCG K +F P
Sbjct: 3 QKYVCNVCGYEYDPAEHDNVPFDQLPDDWCCPVCGVSKDQFSP 45
>pdb|1BQ8|A Chain A, Rubredoxin (Methionine Mutant) From Pyrococcus Furiosus
pdb|3RYG|A Chain A, 128 Hours Neutron Structure Of Perdeuterated Rubredoxin
pdb|3RZ6|A Chain A, Neutron Structure Of Perdeuterated Rubredoxin Using 40
Hours 1st Pass Data
pdb|3RZT|A Chain A, Neutron Structure Of Perdeuterated Rubredoxin Using Rapid
(14 Hours) Data
pdb|3SS2|A Chain A, Neutron Structure Of Perdeuterated Rubredoxin Using 48
Hours 3rd Pass Data
Length = 54
Score = 48.1 bits (113), Expect = 2e-06, Method: Composition-based stats.
Identities = 19/46 (41%), Positives = 28/46 (60%), Gaps = 11/46 (23%)
Query: 79 YICRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRF 113
++C+ CGYIY+E F++LPD++ CP+CGAPK F
Sbjct: 4 WVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEF 49
>pdb|1BQ9|A Chain A, Rubredoxin (Formyl Methionine Mutant) From Pyrococcus
Furiosus
pdb|3KYW|A Chain A, Xray Crystal Structure Determination Of H-Labeled
Perdeuterated Rubredoxin At 295k
pdb|3KYX|A Chain A, Joint XrayNEUTRON CRYSTAL STRUCTURE DETERMINATION OF FULLY
Perdeuterated Rubredoxin At 295k
pdb|3KYY|A Chain A, Joint XrayNEUTRON CRYSTAL STRUCTURE DETERMINATION OF
H-Labeled Perdeuterated Rubredoxin At 295k
Length = 54
Score = 47.8 bits (112), Expect = 3e-06, Method: Composition-based stats.
Identities = 19/46 (41%), Positives = 28/46 (60%), Gaps = 11/46 (23%)
Query: 79 YICRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRF 113
++C+ CGYIY+E F++LPD++ CP+CGAPK F
Sbjct: 4 WVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEF 49
>pdb|1BRF|A Chain A, Rubredoxin (Wild Type) From Pyrococcus Furiosus
pdb|1CAA|A Chain A, X-Ray Crystal Structures Of The Oxidized And Reduced Forms
Of The Rubredoxin From The Marine Hyperthermophilic
Archaebacterium Pyrococcus Furiosus
pdb|1CAD|A Chain A, X-Ray Crystal Structures Of The Oxidized And Reduced Forms
Of The Rubredoxin From The Marine Hyperthermophilic
Archaebacterium Pyrococcus Furiosus
pdb|1ZRP|A Chain A, Solution-State Structure By Nmr Of Zinc-Substituted
Rubredoxin From The Marine Hyperthermophilic
Archaebacterium Pyrococcus Furiosus
pdb|1VCX|A Chain A, Neutron Crystal Structure Of The Wild Type Rubredoxin From
Pyrococcus Furiosus At 1.5a Resolution
Length = 53
Score = 47.8 bits (112), Expect = 3e-06, Method: Composition-based stats.
Identities = 19/46 (41%), Positives = 28/46 (60%), Gaps = 11/46 (23%)
Query: 79 YICRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRF 113
++C+ CGYIY+E F++LPD++ CP+CGAPK F
Sbjct: 3 WVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEF 48
>pdb|1IU5|A Chain A, X-Ray Crystal Structure Of The Rubredoxin Mutant From
Pyrococcus Furiosus
pdb|1RWD|A Chain A, Backbone Nmr Structure Of A Mutant P. Furiosus Rubredoxin
Using Residual Dipolar Couplings
pdb|1IU6|A Chain A, Neutron Crystal Structure Of The Rubredoxin Mutant From
Pyrococcus Furiosus
Length = 53
Score = 47.8 bits (112), Expect = 3e-06, Method: Composition-based stats.
Identities = 19/46 (41%), Positives = 28/46 (60%), Gaps = 11/46 (23%)
Query: 79 YICRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRF 113
Y+C+ CGYIY+E F+++PD++ CP+CGAPK F
Sbjct: 3 YVCKICGYIYDEDAGDPDNGVSPGTKFEEIPDDWVCPICGAPKSEF 48
>pdb|3KYU|A Chain A, X-Ray Crystal Structure Determination Of Fully
Perdeuterated Rubredoxin At 100k
pdb|3KYV|A Chain A, Denovo X-Ray Crystal Structure Determination Of H-Labeled
Perdeuterated Rubredoxin At 100k
pdb|4AR5|A Chain A, X-ray Crystallographic Structure Of The Oxidised Form
Perdeuterated Pyrococcus Furiosus Rubredoxin In D2o At
295k (in Quartz Capillary) To 1.00 Angstrom Resolution.
pdb|4AR6|A Chain A, X-ray Crystallographic Structure Of The Reduced Form
Perdeuterated Pyrococcus Furiosus Rubredoxin At 295 K
(in Quartz Capillary) To 0.92 Angstroms Resolution.
pdb|4AR3|A Chain A, Near-atomic Resolution Neutron Crystallography On The
Oxidised Form Perdeuterated Pyrococcus Furiosus
Rubredoxin.
pdb|4AR4|A Chain A, Neutron Crystallographic Structure Of The Reduced Form
Perdeuterated Pyrococcus Furiosus Rubredoxin To 1.38
Angstroms Resolution
Length = 54
Score = 47.8 bits (112), Expect = 3e-06, Method: Composition-based stats.
Identities = 19/46 (41%), Positives = 28/46 (60%), Gaps = 11/46 (23%)
Query: 79 YICRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRF 113
++C+ CGYIY+E F++LPD++ CP+CGAPK F
Sbjct: 4 WVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEF 49
>pdb|1YK5|A Chain A, Pyrococcus Abyssi Rubredoxin
pdb|1YK5|B Chain B, Pyrococcus Abyssi Rubredoxin
pdb|1YK5|C Chain C, Pyrococcus Abyssi Rubredoxin
pdb|1YK5|D Chain D, Pyrococcus Abyssi Rubredoxin
Length = 53
Score = 44.3 bits (103), Expect = 3e-05, Method: Composition-based stats.
Identities = 19/44 (43%), Positives = 26/44 (59%), Gaps = 11/44 (25%)
Query: 81 CRDCGYIYNERK-----------PFDQLPDNYFCPVCGAPKRRF 113
C+ CGYIY+E + F+ LPD++ CP+CGAPK F
Sbjct: 6 CKICGYIYDEDEGDPDNGISPGTKFEDLPDDWVCPLCGAPKSEF 49
>pdb|2PVE|A Chain A, Nmr And X-Ray Analysis Of Structural Additivity In Metal
Binding Site-Swapped Hybrids Of Rubredoxin
pdb|2PVE|B Chain B, Nmr And X-Ray Analysis Of Structural Additivity In Metal
Binding Site-Swapped Hybrids Of Rubredoxin
pdb|2PVE|C Chain C, Nmr And X-Ray Analysis Of Structural Additivity In Metal
Binding Site-Swapped Hybrids Of Rubredoxin
Length = 54
Score = 44.3 bits (103), Expect = 4e-05, Method: Composition-based stats.
Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 11/48 (22%)
Query: 77 QAYICRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRF 113
+ Y C+ CGYIYN F +PD++ CP+CGAPK F
Sbjct: 2 KKYTCKICGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPICGAPKSEF 49
>pdb|1YK4|A Chain A, Ultra-High Resolution Structure Of Pyrococcus Abyssi
Rubredoxin W4lR5S
Length = 52
Score = 43.9 bits (102), Expect = 4e-05, Method: Composition-based stats.
Identities = 19/44 (43%), Positives = 26/44 (59%), Gaps = 11/44 (25%)
Query: 81 CRDCGYIYNERK-----------PFDQLPDNYFCPVCGAPKRRF 113
C+ CGYIY+E + F+ LPD++ CP+CGAPK F
Sbjct: 5 CKICGYIYDEDEGDPDNGISPGTKFEDLPDDWVCPLCGAPKSEF 48
>pdb|2PYA|A Chain A, Ultra-high Resolution Structure Of P. Abyssi Rubredoxin
W4l/r5s/a44s
Length = 52
Score = 43.1 bits (100), Expect = 8e-05, Method: Composition-based stats.
Identities = 18/44 (40%), Positives = 26/44 (59%), Gaps = 11/44 (25%)
Query: 81 CRDCGYIYNERK-----------PFDQLPDNYFCPVCGAPKRRF 113
C+ CGYIY+E + F+ LPD++ CP+CG+PK F
Sbjct: 5 CKICGYIYDEDEGDPDNGISPGTKFEDLPDDWVCPLCGSPKSEF 48
>pdb|2PVX|A Chain A, Nmr And X-ray Analysis Of Structural Additivity In Metal
Binding Site-swapped Hybrids Of Rubredoxin
pdb|2PVX|B Chain B, Nmr And X-ray Analysis Of Structural Additivity In Metal
Binding Site-swapped Hybrids Of Rubredoxin
pdb|2PVX|C Chain C, Nmr And X-ray Analysis Of Structural Additivity In Metal
Binding Site-swapped Hybrids Of Rubredoxin
pdb|2PVX|D Chain D, Nmr And X-ray Analysis Of Structural Additivity In Metal
Binding Site-swapped Hybrids Of Rubredoxin
pdb|2PVX|E Chain E, Nmr And X-ray Analysis Of Structural Additivity In Metal
Binding Site-swapped Hybrids Of Rubredoxin
pdb|2PVX|F Chain F, Nmr And X-ray Analysis Of Structural Additivity In Metal
Binding Site-swapped Hybrids Of Rubredoxin
pdb|2PVX|G Chain G, Nmr And X-ray Analysis Of Structural Additivity In Metal
Binding Site-swapped Hybrids Of Rubredoxin
pdb|2PVX|H Chain H, Nmr And X-ray Analysis Of Structural Additivity In Metal
Binding Site-swapped Hybrids Of Rubredoxin
Length = 54
Score = 42.4 bits (98), Expect = 1e-04, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 11/48 (22%)
Query: 77 QAYICRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRF 113
+ ++C CGYIY+E F++LPD++ CP+CG K +F
Sbjct: 2 KKWVCTVCGYIYDEDAGDPDNGISPGTKFEELPDDWVCPLCGVGKDQF 49
>pdb|1T9P|A Chain A, Crystal Structure Of V44a, G45p Cp Rubredoxin
pdb|1T9P|B Chain B, Crystal Structure Of V44a, G45p Cp Rubredoxin
pdb|1T9P|C Chain C, Crystal Structure Of V44a, G45p Cp Rubredoxin
Length = 54
Score = 42.4 bits (98), Expect = 1e-04, Method: Composition-based stats.
Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 11/48 (22%)
Query: 77 QAYICRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRF 113
+ Y C CGYIYN F +PD++ CP+CGAPK +F
Sbjct: 2 KKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGAPKDQF 49
>pdb|1SPW|A Chain A, Solution Structure Of A Loop Truncated Mutant From D.
Gigas Rubredoxin, Nmr
Length = 39
Score = 42.0 bits (97), Expect = 2e-04, Method: Composition-based stats.
Identities = 18/35 (51%), Positives = 23/35 (65%), Gaps = 2/35 (5%)
Query: 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRF 113
Y+C CGY Y+ F+ LPD++ CPVCGA K F
Sbjct: 4 YVCTVCGYEYD--PAFEDLPDDWACPVCGASKDAF 36
>pdb|2QL0|A Chain A, Zinc-Substituted Rubredoxin From Desulfovibrio Vulgaris
Length = 52
Score = 40.4 bits (93), Expect = 5e-04, Method: Composition-based stats.
Identities = 22/48 (45%), Positives = 26/48 (54%), Gaps = 11/48 (22%)
Query: 77 QAYICRDCGYIY--------NERKP---FDQLPDNYFCPVCGAPKRRF 113
+ Y+C CGY Y N KP FD LP ++ CPVCGAPK F
Sbjct: 2 KKYVCTVCGYEYDPAEGDPDNGVKPGTSFDDLPADWVCPVCGAPKSEF 49
>pdb|8RXN|A Chain A, Refinement Of Rubredoxin From Desulfovibrio Vulgaris At
1.0 Angstroms With And Without Restraints
pdb|7RXN|A Chain A, Structure Of Rubredoxin From Desulfovibrio Vulgaris At 1.5
A Resolution
pdb|2KKD|A Chain A, Nmr Structure Of Ni Substitued Desulfovibrio Vulgaris
Rubredoxin
Length = 52
Score = 40.0 bits (92), Expect = 6e-04, Method: Composition-based stats.
Identities = 22/48 (45%), Positives = 26/48 (54%), Gaps = 11/48 (22%)
Query: 77 QAYICRDCGYIY--------NERKP---FDQLPDNYFCPVCGAPKRRF 113
+ Y+C CGY Y N KP FD LP ++ CPVCGAPK F
Sbjct: 2 KKYVCTVCGYEYDPAEGDPDNGVKPGTSFDDLPADWVCPVCGAPKSEF 49
>pdb|1RB9|A Chain A, Rubredoxin From Desulfovibrio Vulgaris Refined
Anisotropically At 0.92 Angstroms Resolution
Length = 52
Score = 39.7 bits (91), Expect = 8e-04, Method: Composition-based stats.
Identities = 22/48 (45%), Positives = 26/48 (54%), Gaps = 11/48 (22%)
Query: 77 QAYICRDCGYIY--------NERKP---FDQLPDNYFCPVCGAPKRRF 113
+ Y+C CGY Y N KP FD LP ++ CPVCGAPK F
Sbjct: 2 KKYVCTVCGYEYDPAEGDPDNGVKPGTSFDDLPADWVCPVCGAPKSEF 49
>pdb|1NNQ|A Chain A, Rubrerythrin From Pyrococcus Furiosus Pfu-1210814
pdb|1NNQ|B Chain B, Rubrerythrin From Pyrococcus Furiosus Pfu-1210814
pdb|2HR5|A Chain A, Pf1283- Rubrerythrin From Pyrococcus Furiosus Iron Bound
Form
pdb|2HR5|B Chain B, Pf1283- Rubrerythrin From Pyrococcus Furiosus Iron Bound
Form
Length = 171
Score = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 7/41 (17%)
Query: 73 VASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRF 113
+ K+ YIC CGY D+ P+ +CPVCGAPK +F
Sbjct: 134 IEIKKVYICPICGYT-----AVDEAPE--YCPVCGAPKEKF 167
>pdb|3MPS|A Chain A, Peroxide Bound Oxidized Rubrerythrin From Pyrococcus
Furiosus
pdb|3MPS|B Chain B, Peroxide Bound Oxidized Rubrerythrin From Pyrococcus
Furiosus
pdb|3MPS|D Chain D, Peroxide Bound Oxidized Rubrerythrin From Pyrococcus
Furiosus
pdb|3MPS|F Chain F, Peroxide Bound Oxidized Rubrerythrin From Pyrococcus
Furiosus
pdb|3MPS|G Chain G, Peroxide Bound Oxidized Rubrerythrin From Pyrococcus
Furiosus
pdb|3MPS|H Chain H, Peroxide Bound Oxidized Rubrerythrin From Pyrococcus
Furiosus
pdb|3MPS|I Chain I, Peroxide Bound Oxidized Rubrerythrin From Pyrococcus
Furiosus
pdb|3MPS|K Chain K, Peroxide Bound Oxidized Rubrerythrin From Pyrococcus
Furiosus
pdb|3PWF|A Chain A, High Resolution Structure Of The Fully Reduced Form Of
Rubrerythrin From P. Furiosus
pdb|3PWF|B Chain B, High Resolution Structure Of The Fully Reduced Form Of
Rubrerythrin From P. Furiosus
pdb|3PZA|A Chain A, Fully Reduced (All-Ferrous) Pyrococcus Rubrerythrin After
A 10 Second Exposure To Peroxide.
pdb|3PZA|B Chain B, Fully Reduced (All-Ferrous) Pyrococcus Rubrerythrin After
A 10 Second Exposure To Peroxide.
pdb|3QVD|A Chain A, Exposure Of Rubrerythrin From Pyrococcus Furiosus To
Peroxide, Fifteen Second Time Point.
pdb|3QVD|B Chain B, Exposure Of Rubrerythrin From Pyrococcus Furiosus To
Peroxide, Fifteen Second Time Point.
pdb|3QVD|C Chain C, Exposure Of Rubrerythrin From Pyrococcus Furiosus To
Peroxide, Fifteen Second Time Point.
pdb|3QVD|D Chain D, Exposure Of Rubrerythrin From Pyrococcus Furiosus To
Peroxide, Fifteen Second Time Point.
pdb|3QVD|E Chain E, Exposure Of Rubrerythrin From Pyrococcus Furiosus To
Peroxide, Fifteen Second Time Point.
pdb|3QVD|F Chain F, Exposure Of Rubrerythrin From Pyrococcus Furiosus To
Peroxide, Fifteen Second Time Point.
pdb|3QVD|G Chain G, Exposure Of Rubrerythrin From Pyrococcus Furiosus To
Peroxide, Fifteen Second Time Point.
pdb|3QVD|H Chain H, Exposure Of Rubrerythrin From Pyrococcus Furiosus To
Peroxide, Fifteen Second Time Point
Length = 170
Score = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 7/41 (17%)
Query: 73 VASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRF 113
+ K+ YIC CGY D+ P+ +CPVCGAPK +F
Sbjct: 133 IEIKKVYICPICGYT-----AVDEAPE--YCPVCGAPKEKF 166
>pdb|1C09|A Chain A, Rubredoxin V44a Cp
pdb|1C09|B Chain B, Rubredoxin V44a Cp
pdb|1C09|C Chain C, Rubredoxin V44a Cp
Length = 54
Score = 39.3 bits (90), Expect = 0.001, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 11/48 (22%)
Query: 77 QAYICRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRF 113
+ Y C CGYIYN F +PD++ CP+CGA K +F
Sbjct: 2 KKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGAGKDQF 49
>pdb|2RDV|A Chain A, Rubredoxin From Desulfovibrio Vulgaris Miyazaki F,
Monoclinic Crystal Form
pdb|2RDV|B Chain B, Rubredoxin From Desulfovibrio Vulgaris Miyazaki F,
Monoclinic Crystal Form
pdb|2RDV|C Chain C, Rubredoxin From Desulfovibrio Vulgaris Miyazaki F,
Monoclinic Crystal Form
pdb|1RDV|A Chain A, Rubredoxin From Desulfovibrio Vulgaris Miyazaki F,
Trigonal Crystal Form
Length = 52
Score = 38.9 bits (89), Expect = 0.001, Method: Composition-based stats.
Identities = 20/50 (40%), Positives = 27/50 (54%), Gaps = 11/50 (22%)
Query: 77 QAYICRDCGYIY--------NERKP---FDQLPDNYFCPVCGAPKRRFRP 115
+ Y+C CGY Y N KP F+ +P ++ CP+CGAPK F P
Sbjct: 2 KKYVCTVCGYEYDPAEGDPDNGVKPGTAFEDVPADWVCPICGAPKSEFEP 51
>pdb|4RXN|A Chain A, Crystallographic Refinement Of Rubredoxin At 1.2 Angstroms
Resolution
pdb|5RXN|A Chain A, Combined Crystallographic Refinement And Energy
Minimization Of Rubredoxin At 1.2 Angstrom Resolution
Length = 54
Score = 38.5 bits (88), Expect = 0.002, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 11/48 (22%)
Query: 77 QAYICRDCGYIY-----------NERKPFDQLPDNYFCPVCGAPKRRF 113
+ Y C CGYIY N F +PD++ CP+CG K F
Sbjct: 2 KKYTCTVCGYIYDPEDGDPDDGVNPGTDFKDIPDDWVCPLCGVGKDEF 49
>pdb|1FHH|A Chain A, X-Ray Crystal Structure Of Oxidized Rubredoxin
pdb|1FHM|A Chain A, X-Ray Crystal Structure Of Reduced Rubredoxin
pdb|1R0F|A Chain A, Gallium-Substituted Rubredoxin
pdb|1R0G|A Chain A, Mercury-Substituted Rubredoxin
pdb|1R0H|A Chain A, Cobalt-Substituted Rubredoxin
pdb|1R0I|A Chain A, Cadmium-Substituted Rubredoxin
pdb|1R0J|A Chain A, Nickel-Substituted Rubredoxin
pdb|1IRN|A Chain A, Rubredoxin (zn-substituted) At 1.2 Angstroms Resolution
pdb|1IRO|A Chain A, Rubredoxin (Oxidized, Fe(Iii)) At 1.1 Angstroms Resolution
Length = 54
Score = 38.1 bits (87), Expect = 0.002, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 11/48 (22%)
Query: 77 QAYICRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRF 113
+ Y C CGYIYN F +PD++ CP+CG K +F
Sbjct: 2 KKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQF 49
>pdb|2DSX|A Chain A, Crystal Structure Of Rubredoxin From Desulfovibrio Gigas
To Ultra-high 0.68 A Resolution
pdb|1RDG|A Chain A, Rubredoxin From Desulfovibrio Gigas. A Molecular Model Of
The Oxidized Form At 1.4 Angstroms Resolution
pdb|1E8J|A Chain A, Solution Structure Of Desulfovibrio Gigas Zinc Rubredoxin,
Nmr, 20 Structures
Length = 52
Score = 38.1 bits (87), Expect = 0.002, Method: Composition-based stats.
Identities = 19/46 (41%), Positives = 24/46 (52%), Gaps = 11/46 (23%)
Query: 79 YICRDCGYIYNERK-----------PFDQLPDNYFCPVCGAPKRRF 113
Y+C CGY Y+ K F+ LPD++ CPVCGA K F
Sbjct: 4 YVCTVCGYEYDPAKGDPDSGIKPGTKFEDLPDDWACPVCGASKDAF 49
>pdb|1T9O|A Chain A, Crystal Structure Of V44g Cp Rubredoxin
pdb|1T9O|B Chain B, Crystal Structure Of V44g Cp Rubredoxin
pdb|1T9O|C Chain C, Crystal Structure Of V44g Cp Rubredoxin
Length = 54
Score = 38.1 bits (87), Expect = 0.002, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 11/48 (22%)
Query: 77 QAYICRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRF 113
+ Y C CGYIYN F +PD++ CP+CG K +F
Sbjct: 2 KKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGGGKDQF 49
>pdb|1BFY|A Chain A, Solution Structure Of Reduced Clostridium Pasteurianum
Rubredoxin, Nmr, 20 Structures
Length = 54
Score = 38.1 bits (87), Expect = 0.002, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 11/48 (22%)
Query: 77 QAYICRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRF 113
+ Y C CGYIYN F +PD++ CP+CG K +F
Sbjct: 2 KKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQF 49
>pdb|1T9Q|A Chain A, Crystal Structure Of V44l Cp Rubredoxin
Length = 54
Score = 37.7 bits (86), Expect = 0.003, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 11/48 (22%)
Query: 77 QAYICRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRF 113
+ Y C CGYIYN F +PD++ CP+CG K +F
Sbjct: 2 KKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGLGKDQF 49
>pdb|1SMM|A Chain A, Crystal Structure Of Cp Rd L41a Mutant In Oxidized State
pdb|1SMU|A Chain A, Crystal Structure Of Cp Rd L41a Mutant In Reduced State 1
(Drop-Reduced)
pdb|1SMW|A Chain A, Crystal Structure Of Cp Rd L41a Mutant In Reduced State 2
(Soaked)
Length = 54
Score = 37.4 bits (85), Expect = 0.004, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 11/48 (22%)
Query: 77 QAYICRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRF 113
+ Y C CGYIYN F +PD++ CP CG K +F
Sbjct: 2 KKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPACGVGKDQF 49
>pdb|1DX8|A Chain A, Rubredoxin From Guillardia Theta
Length = 70
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 11/47 (23%)
Query: 79 YICRDCGYIYNERK-----------PFDQLPDNYFCPVCGAPKRRFR 114
Y C CGYIY K PF L D++ CP C +PK +F+
Sbjct: 8 YECEACGYIYEPEKGDKFAGIPPGTPFVDLSDSFMCPACRSPKNQFK 54
>pdb|1H7V|A Chain A, Rubredoxin From Guillardia Theta
Length = 60
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 11/47 (23%)
Query: 79 YICRDCGYIYNERK-----------PFDQLPDNYFCPVCGAPKRRFR 114
Y C CGYIY K PF L D++ CP C +PK +F+
Sbjct: 8 YECEACGYIYEPEKGDKFAGIPPGTPFVDLSDSFMCPACRSPKNQFK 54
>pdb|1S24|A Chain A, Rubredoxin Domain Ii From Pseudomonas Oleovorans
Length = 87
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 11/49 (22%)
Query: 79 YICRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRFRPY 116
+IC CG+IY+E F+ +PD++ CP CGA K + Y
Sbjct: 36 WICITCGHIYDEALGDEAEGFTPGTRFEDIPDDWCCPDCGATKEDYVLY 84
>pdb|1B13|A Chain A, Clostridium Pasteurianum Rubredoxin G10a Mutant
Length = 54
Score = 35.8 bits (81), Expect = 0.012, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 11/48 (22%)
Query: 77 QAYICRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRF 113
+ Y C C YIYN F +PD++ CP+CG K +F
Sbjct: 2 KKYTCTVCAYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQF 49
>pdb|1B2J|A Chain A, Clostridium Pasteurianum Rubredoxin G43a Mutant
Length = 54
Score = 35.8 bits (81), Expect = 0.012, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 11/48 (22%)
Query: 77 QAYICRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRF 113
+ Y C CGYIYN F +PD++ CP+C K +F
Sbjct: 2 KKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCAVGKDQF 49
>pdb|1BE7|A Chain A, Clostridium Pasteurianum Rubredoxin C42s Mutant
Length = 54
Score = 34.7 bits (78), Expect = 0.028, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 11/48 (22%)
Query: 77 QAYICRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRF 113
+ Y C CGYIYN F +PD++ CP+ G K +F
Sbjct: 2 KKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLSGVGKDQF 49
>pdb|2KN9|A Chain A, Solution Structure Of Zinc-Substituted Rubredoxin B
(Rv3250c) From Mycobacterium Tuberculosis. Seattle
Structural Genomics Center For Infectious Disease Target
Mytud.01635.A
Length = 81
Score = 33.1 bits (74), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 11/45 (24%)
Query: 81 CRDCGYIYNERKPF-----------DQLPDNYFCPVCGAPKRRFR 114
C CG+ Y+E + D +PD++ CP CGA K F
Sbjct: 30 CIQCGFEYDEALGWPEDGIAAGTRWDDIPDDWSCPDCGAAKSDFE 74
>pdb|1QCV|A Chain A, Rubredoxin Variant (Pfrd-Xc4) Folds Without Iron
Length = 53
Score = 33.1 bits (74), Expect = 0.084, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 11/46 (23%)
Query: 79 YICRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRF 113
++ + GYIY+E F++LPD++ P+ GAPK F
Sbjct: 3 WVLKITGYIYDEDAGDPDNGISPGTKFEELPDDWVAPITGAPKSEF 48
>pdb|1B2O|A Chain A, Clostridium Pasteurianum Rubredoxin G10vg43a Mutant
pdb|1B2O|B Chain B, Clostridium Pasteurianum Rubredoxin G10vg43a Mutant
Length = 54
Score = 32.7 bits (73), Expect = 0.11, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 11/48 (22%)
Query: 77 QAYICRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRF 113
+ Y C C YIYN F +PD++ CP+C K +F
Sbjct: 2 KKYTCTVCVYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCAVGKDQF 49
>pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP
CLAMP DOMAIN
Length = 436
Score = 31.2 bits (69), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 4/35 (11%)
Query: 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKR 111
+ ++C +CG+I E D+ +CPVCG +R
Sbjct: 4 EVWVCENCGHIALE----DKRRRRVYCPVCGEEER 34
>pdb|1GKU|B Chain B, Reverse Gyrase From Archaeoglobus Fulgidus
Length = 1054
Score = 28.9 bits (63), Expect = 1.4, Method: Composition-based stats.
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 8/28 (28%)
Query: 81 CRDCGYIYNERKPFDQLPDNYFCPVCGA 108
CRDCGY + E D CP CG+
Sbjct: 584 CRDCGYQFTE--------DRESCPKCGS 603
>pdb|1GL9|B Chain B, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
pdb|1GL9|C Chain C, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
Length = 1054
Score = 28.9 bits (63), Expect = 1.5, Method: Composition-based stats.
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 8/28 (28%)
Query: 81 CRDCGYIYNERKPFDQLPDNYFCPVCGA 108
CRDCGY + E D CP CG+
Sbjct: 584 CRDCGYQFTE--------DRESCPKCGS 603
>pdb|4DDT|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 2
pdb|4DDU|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 1
pdb|4DDV|A Chain A, Thermotoga Maritima Reverse Gyrase, Triclinic Form
pdb|4DDV|B Chain B, Thermotoga Maritima Reverse Gyrase, Triclinic Form
pdb|4DDW|A Chain A, Thermotoga Maritima Reverse Gyrase, C-centered
Orthorhombic Form
pdb|4DDX|A Chain A, Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic
Form
pdb|4DDX|B Chain B, Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic
Form
Length = 1104
Score = 28.5 bits (62), Expect = 2.1, Method: Composition-based stats.
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 8/28 (28%)
Query: 81 CRDCGYIYNERKPFDQLPDNYFCPVCGA 108
CRDCGY + E D CPVC +
Sbjct: 621 CRDCGYQFTE--------DRDECPVCSS 640
>pdb|2V3B|B Chain B, Crystal Structure Of The Electron Transfer Complex
Rubredoxin - Rubredoxin Reductase From Pseudomonas
Aeruginosa
Length = 55
Score = 27.7 bits (60), Expect = 3.4, Method: Composition-based stats.
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 11/44 (25%)
Query: 81 CRDCGYIYNER-----------KPFDQLPDNYFCPVCGAPKRRF 113
C CG+IY+E ++ +P ++ CP CG K F
Sbjct: 6 CVVCGFIYDEALGLPEEGIPAGTRWEDIPADWVCPDCGVGKIDF 49
>pdb|2PMZ|B Chain B, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|R Chain R, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|B Chain B, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|J Chain J, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 1124
Score = 27.3 bits (59), Expect = 4.3, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 4/35 (11%)
Query: 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRF 113
Y+C CGYI +D+ + Y CP+ G F
Sbjct: 1059 YVCDQCGYI----GWYDKNKNKYVCPIHGDKSNLF 1089
>pdb|2WAQ|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|R Chain R, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|B Chain B, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|R Chain R, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|B Chain B, Rnap At 3.2ang
pdb|4B1O|B Chain B, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|R Chain R, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 1131
Score = 27.3 bits (59), Expect = 4.6, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 4/35 (11%)
Query: 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRF 113
Y+C CGYI +D+ + Y CP+ G F
Sbjct: 1062 YVCDQCGYI----GWYDKNKNKYVCPIHGDKSNLF 1092
>pdb|1B71|A Chain A, Rubrerythrin
pdb|1DVB|A Chain A, Rubrerythrin
pdb|1JYB|A Chain A, Crystal Structure Of Rubrerythrin
pdb|1LKM|A Chain A, Crystal Structure Of Desulfovibrio Vulgaris Rubrerythrin
All-Iron(Iii) Form
pdb|1LKO|A Chain A, Crystal Structure Of Desulfovibrio Vulgaris Rubrerythrin
All-iron(ii) Form
pdb|1LKP|A Chain A, Crystal Structure Of Desulfovibrio Vulgaris Rubrerythrin
All-iron(ii) Form, Azide Adduct
pdb|1QYB|A Chain A, X-Ray Crystal Structure Of Desulfovibrio Vulgaris
Rubrerythrin With Zinc Substituted Into The [fe(Scys)4]
Site And Alternative Diiron Site Structures
pdb|1S2Z|A Chain A, X-Ray Crystal Structure Of Desulfovibrio Vulgaris
Rubrerythrin With Displacement Of Iron By Zinc At The
Diiron Site
pdb|1S30|A Chain A, X-Ray Crystal Structure Of Desulfovibrio Vulgaris
Rubrerythrin With Displacement Of Iron By Zinc At The
Diiron Site
Length = 191
Score = 26.9 bits (58), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 6/36 (16%)
Query: 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFR 114
+ CR+CGY++ P+ CP C PK F
Sbjct: 156 WRCRNCGYVHEGTGA----PE--LCPACAHPKAHFE 185
>pdb|1RYT|A Chain A, Rubrerythrin
Length = 190
Score = 26.9 bits (58), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 6/36 (16%)
Query: 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFR 114
+ CR+CGY++ P+ CP C PK F
Sbjct: 155 WRCRNCGYVHEGTGA----PE--LCPACAHPKAHFE 184
>pdb|1YUX|A Chain A, Mixed Valant State Of Nigerythrin
pdb|1YUX|B Chain B, Mixed Valant State Of Nigerythrin
pdb|1YV1|A Chain A, Fully Reduced State Of Nigerythrin (All Ferrous)
pdb|1YV1|B Chain B, Fully Reduced State Of Nigerythrin (All Ferrous)
Length = 202
Score = 26.9 bits (58), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 7/38 (18%)
Query: 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRPY 116
++C CGYI+ + + F++ CP+C PK F Y
Sbjct: 172 HLCPICGYIH-KGEDFEK------CPICFRPKDTFTAY 202
>pdb|1YUZ|A Chain A, Partially Reduced State Of Nigerythrin
pdb|1YUZ|B Chain B, Partially Reduced State Of Nigerythrin
Length = 202
Score = 26.9 bits (58), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 7/38 (18%)
Query: 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRPY 116
++C CGYI+ + + F++ CP+C PK F Y
Sbjct: 172 HLCPICGYIH-KGEDFEK------CPICFRPKDTFTAY 202
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
0.321 0.136 0.424
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,902,428
Number of Sequences: 62578
Number of extensions: 123265
Number of successful extensions: 359
Number of sequences better than 100.0: 48
Number of HSP's better than 100.0 without gapping: 35
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 285
Number of HSP's gapped (non-prelim): 49
length of query: 169
length of database: 14,973,337
effective HSP length: 92
effective length of query: 77
effective length of database: 9,216,161
effective search space: 709644397
effective search space used: 709644397
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: 48 (23.1 bits)