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= 038893
(235 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 20/52 (38%), Positives = 25/52 (48%), Gaps = 11/52 (21%)
Query: 159 ATHICLDCGYIYFLQ-----------KPFDELPDTYVCPQCQAPKKRFARYD 199
A +C CGYIY F+ELPD +VCP C APK F + +
Sbjct: 2 AKWVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEFEKLE 53
>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 = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 11/52 (21%)
Query: 159 ATHICLDCGYIYFLQ-----------KPFDELPDTYVCPQCQAPKKRFARYD 199
A ++C CGYIY F+E+PD +VCP C APK F + +
Sbjct: 1 AKYVCKICGYIYDEDAGDPDNGVSPGTKFEEIPDDWVCPICGAPKSEFEKLE 52
>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 = 39.3 bits (90), Expect = 0.002, Method: Composition-based stats.
Identities = 20/52 (38%), Positives = 25/52 (48%), Gaps = 11/52 (21%)
Query: 159 ATHICLDCGYIYFLQ-----------KPFDELPDTYVCPQCQAPKKRFARYD 199
A +C CGYIY F+ELPD +VCP C APK F + +
Sbjct: 2 AKWVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEFEKLE 53
>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 = 39.3 bits (90), Expect = 0.002, Method: Composition-based stats.
Identities = 20/52 (38%), Positives = 25/52 (48%), Gaps = 11/52 (21%)
Query: 159 ATHICLDCGYIYFLQ-----------KPFDELPDTYVCPQCQAPKKRFARYD 199
A +C CGYIY F+ELPD +VCP C APK F + +
Sbjct: 2 AKWVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEFEKLE 53
>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 = 39.3 bits (90), Expect = 0.002, Method: Composition-based stats.
Identities = 20/52 (38%), Positives = 25/52 (48%), Gaps = 11/52 (21%)
Query: 159 ATHICLDCGYIYFLQ-----------KPFDELPDTYVCPQCQAPKKRFARYD 199
A +C CGYIY F+ELPD +VCP C APK F + +
Sbjct: 1 AKWVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEFEKLE 52
>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 = 38.9 bits (89), Expect = 0.002, Method: Composition-based stats.
Identities = 19/48 (39%), Positives = 24/48 (50%), Gaps = 11/48 (22%)
Query: 163 CLDCGYIYFLQK-----------PFDELPDTYVCPQCQAPKKRFARYD 199
C CGYIY + F++LPD +VCP C APK F R +
Sbjct: 6 CKICGYIYDEDEGDPDNGISPGTKFEDLPDDWVCPLCGAPKSEFERIE 53
>pdb|1YK4|A Chain A, Ultra-High Resolution Structure Of Pyrococcus Abyssi
Rubredoxin W4lR5S
Length = 52
Score = 38.5 bits (88), Expect = 0.004, Method: Composition-based stats.
Identities = 19/48 (39%), Positives = 24/48 (50%), Gaps = 11/48 (22%)
Query: 163 CLDCGYIYFLQK-----------PFDELPDTYVCPQCQAPKKRFARYD 199
C CGYIY + F++LPD +VCP C APK F R +
Sbjct: 5 CKICGYIYDEDEGDPDNGISPGTKFEDLPDDWVCPLCGAPKSEFERIE 52
>pdb|1H7V|A Chain A, Rubredoxin From Guillardia Theta
Length = 60
Score = 38.1 bits (87), Expect = 0.005, Method: Composition-based stats.
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 11/44 (25%)
Query: 163 CLDCGYIYFLQK-----------PFDELPDTYVCPQCQAPKKRF 195
C CGYIY +K PF +L D+++CP C++PK +F
Sbjct: 10 CEACGYIYEPEKGDKFAGIPPGTPFVDLSDSFMCPACRSPKNQF 53
>pdb|1DX8|A Chain A, Rubredoxin From Guillardia Theta
Length = 70
Score = 37.7 bits (86), Expect = 0.006, Method: Composition-based stats.
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 11/44 (25%)
Query: 163 CLDCGYIYFLQK-----------PFDELPDTYVCPQCQAPKKRF 195
C CGYIY +K PF +L D+++CP C++PK +F
Sbjct: 10 CEACGYIYEPEKGDKFAGIPPGTPFVDLSDSFMCPACRSPKNQF 53
>pdb|6RXN|A Chain A, The Structure Of Rubredoxin From Desulfovibrio
Desulfuricans
Length = 46
Score = 37.4 bits (85), Expect = 0.007, Method: Composition-based stats.
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 4/40 (10%)
Query: 161 HICLDCGYIYFLQK----PFDELPDTYVCPQCQAPKKRFA 196
++C CGY Y + PFD+LPD + CP C K +F+
Sbjct: 5 YVCNVCGYEYDPAEHDNVPFDQLPDDWCCPVCGVSKDQFS 44
>pdb|2PYA|A Chain A, Ultra-high Resolution Structure Of P. Abyssi Rubredoxin
W4l/r5s/a44s
Length = 52
Score = 37.4 bits (85), Expect = 0.007, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 11/48 (22%)
Query: 163 CLDCGYIYFLQK-----------PFDELPDTYVCPQCQAPKKRFARYD 199
C CGYIY + F++LPD +VCP C +PK F R +
Sbjct: 5 CKICGYIYDEDEGDPDNGISPGTKFEDLPDDWVCPLCGSPKSEFERIE 52
>pdb|1SPW|A Chain A, Solution Structure Of A Loop Truncated Mutant From D.
Gigas Rubredoxin, Nmr
Length = 39
Score = 37.0 bits (84), Expect = 0.009, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 161 HICLDCGYIYFLQKPFDELPDTYVCPQCQAPKKRFAR 197
++C CGY Y F++LPD + CP C A K F +
Sbjct: 4 YVCTVCGYEY--DPAFEDLPDDWACPVCGASKDAFEK 38
>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 = 35.8 bits (81), Expect = 0.022, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 11/46 (23%)
Query: 161 HICLDCGYIYFLQ-----------KPFDELPDTYVCPQCQAPKKRF 195
+ C CGYIY + F ++PD +VCP C APK +F
Sbjct: 4 YTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGAPKDQF 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 = 35.0 bits (79), Expect = 0.037, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 22/46 (47%), Gaps = 11/46 (23%)
Query: 161 HICLDCGYIYFLQ-----------KPFDELPDTYVCPQCQAPKKRF 195
+ C CGYIY + F ++PD +VCP C APK F
Sbjct: 4 YTCKICGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPICGAPKSEF 49
>pdb|1S24|A Chain A, Rubredoxin Domain Ii From Pseudomonas Oleovorans
Length = 87
Score = 34.7 bits (78), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 36/80 (45%), Gaps = 15/80 (18%)
Query: 131 ADVDVKRLPKRPAPPRFGRKLTEAQKARATHICLDCGYIY----------FLQKP-FDEL 179
ADV + L K P R + KA IC+ CG+IY F F+++
Sbjct: 10 ADVKGQDLYKTQPP----RSDAQGGKAYLKWICITCGHIYDEALGDEAEGFTPGTRFEDI 65
Query: 180 PDTYVCPQCQAPKKRFARYD 199
PD + CP C A K+ + Y+
Sbjct: 66 PDDWCCPDCGATKEDYVLYE 85
>pdb|2QL0|A Chain A, Zinc-Substituted Rubredoxin From Desulfovibrio Vulgaris
Length = 52
Score = 33.9 bits (76), Expect = 0.086, Method: Composition-based stats.
Identities = 19/46 (41%), Positives = 23/46 (50%), Gaps = 11/46 (23%)
Query: 161 HICLDCGYIYFLQ--------KP---FDELPDTYVCPQCQAPKKRF 195
++C CGY Y KP FD+LP +VCP C APK F
Sbjct: 4 YVCTVCGYEYDPAEGDPDNGVKPGTSFDDLPADWVCPVCGAPKSEF 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 = 33.5 bits (75), Expect = 0.091, Method: Composition-based stats.
Identities = 19/46 (41%), Positives = 23/46 (50%), Gaps = 11/46 (23%)
Query: 161 HICLDCGYIYFLQ--------KP---FDELPDTYVCPQCQAPKKRF 195
++C CGY Y KP FD+LP +VCP C APK F
Sbjct: 4 YVCTVCGYEYDPAEGDPDNGVKPGTSFDDLPADWVCPVCGAPKSEF 49
>pdb|1RB9|A Chain A, Rubredoxin From Desulfovibrio Vulgaris Refined
Anisotropically At 0.92 Angstroms Resolution
Length = 52
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 23/46 (50%), Gaps = 11/46 (23%)
Query: 161 HICLDCGYIYFLQ--------KP---FDELPDTYVCPQCQAPKKRF 195
++C CGY Y KP FD+LP +VCP C APK F
Sbjct: 4 YVCTVCGYEYDPAEGDPDNGVKPGTSFDDLPADWVCPVCGAPKSEF 49
>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 = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 11/47 (23%)
Query: 162 ICLDCGYIYFLQK-----------PFDELPDTYVCPQCQAPKKRFAR 197
+C CGYIY F+ELPD +VCP C K +F +
Sbjct: 5 VCTVCGYIYDEDAGDPDNGISPGTKFEELPDDWVCPLCGVGKDQFEK 51
>pdb|1UF1|A Chain A, Solution Structure Of The Second Pdz Domain Of Human
Kiaa1526 Protein
Length = 128
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 19/40 (47%), Positives = 26/40 (65%), Gaps = 2/40 (5%)
Query: 55 KPLGLTL--GQKPGGGVVITAVEGGGNAAKAGLKSGDQVL 92
+ LGLT+ G + G G+ IT V+ G A +GLK GDQ+L
Sbjct: 32 RSLGLTIRGGAEYGLGIYITGVDPGSEAEGSGLKVGDQIL 71
>pdb|1UIT|A Chain A, Solution Structure Of Rsgi Ruh-006, The Third Pdz Domain
Of Hdlg5 (Kiaa0583) Protein [homo Sapiens]
Length = 117
Score = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 25/38 (65%)
Query: 55 KPLGLTLGQKPGGGVVITAVEGGGNAAKAGLKSGDQVL 92
+PLG+++ GG+ ++ V G A +AGL+ GDQ+L
Sbjct: 30 EPLGISIVSGEKGGIYVSKVTVGSIAHQAGLEYGDQLL 67
>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 = 32.0 bits (71), Expect = 0.27, Method: Composition-based stats.
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 11/46 (23%)
Query: 161 HICLDCGYIYFLQ-----------KPFDELPDTYVCPQCQAPKKRF 195
+ C CGYIY + F ++PD +VCP C A K +F
Sbjct: 4 YTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGAGKDQF 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 = 31.2 bits (69), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 7/42 (16%)
Query: 158 RATHICLDCGYIYFLQKPFDELPDTYVCPQCQAPKKRFARYD 199
+ +IC CGY DE P+ CP C APK++F ++
Sbjct: 137 KKVYICPICGYT-----AVDEAPE--YCPVCGAPKEKFVVFE 171
>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 = 31.2 bits (69), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 7/42 (16%)
Query: 158 RATHICLDCGYIYFLQKPFDELPDTYVCPQCQAPKKRFARYD 199
+ +IC CGY DE P+ CP C APK++F ++
Sbjct: 136 KKVYICPICGYT-----AVDEAPE--YCPVCGAPKEKFVVFE 170
>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 = 31.2 bits (69), Expect = 0.52, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 11/46 (23%)
Query: 161 HICLDCGYIYFLQ-----------KPFDELPDTYVCPQCQAPKKRF 195
+ C CGYIY + F ++PD +VCP C K F
Sbjct: 4 YTCTVCGYIYDPEDGDPDDGVNPGTDFKDIPDDWVCPLCGVGKDEF 49
>pdb|1B2J|A Chain A, Clostridium Pasteurianum Rubredoxin G43a Mutant
Length = 54
Score = 31.2 bits (69), Expect = 0.54, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 11/46 (23%)
Query: 161 HICLDCGYIYFLQ-----------KPFDELPDTYVCPQCQAPKKRF 195
+ C CGYIY + F ++PD +VCP C K +F
Sbjct: 4 YTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCAVGKDQF 49
>pdb|3K1R|A Chain A, Structure Of Harmonin Npdz1 In Complex With The Sam-Pbm Of
Sans
Length = 192
Score = 31.2 bits (69), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 40/82 (48%), Gaps = 4/82 (4%)
Query: 20 FLAVSKTKNATRSLDNNKITARTAGASKTIEVEVDKPLGLTL----GQKPGGGVVITAVE 75
F A+ ++ +++T R + K + ++ P GL L G + G G+ I+ +
Sbjct: 59 FDAIRPLIPLKHQVEYDQLTPRRSRKLKEVRLDRLHPEGLGLSVRGGLEFGCGLFISHLI 118
Query: 76 GGGNAAKAGLKSGDQVLYTSSF 97
GG A GL+ GD+++ + +
Sbjct: 119 KGGQADSVGLQVGDEIVRINGY 140
>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 = 30.8 bits (68), Expect = 0.60, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 11/48 (22%)
Query: 161 HICLDCGYIYFLQK-----------PFDELPDTYVCPQCQAPKKRFAR 197
++C CGY Y K F++LPD + CP C A K F +
Sbjct: 4 YVCTVCGYEYDPAKGDPDSGIKPGTKFEDLPDDWACPVCGASKDAFEK 51
>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 = 30.8 bits (68), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 11/49 (22%)
Query: 163 CLDCGYIY--FLQKP---------FDELPDTYVCPQCQAPKKRFARYDV 200
C+ CG+ Y L P +D++PD + CP C A K F +V
Sbjct: 30 CIQCGFEYDEALGWPEDGIAAGTRWDDIPDDWSCPDCGAAKSDFEMVEV 78
>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 = 30.8 bits (68), Expect = 0.64, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 11/46 (23%)
Query: 161 HICLDCGYIYFLQ-----------KPFDELPDTYVCPQCQAPKKRF 195
+ C CGYIY + F ++PD +VCP C K +F
Sbjct: 4 YTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPACGVGKDQF 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 = 30.8 bits (68), Expect = 0.74, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 11/46 (23%)
Query: 161 HICLDCGYIYFLQ-----------KPFDELPDTYVCPQCQAPKKRF 195
+ C CGYIY + F ++PD +VCP C K +F
Sbjct: 4 YTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQF 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 = 30.4 bits (67), Expect = 0.81, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 11/46 (23%)
Query: 161 HICLDCGYIYFLQ--------KP---FDELPDTYVCPQCQAPKKRF 195
++C CGY Y KP F+++P +VCP C APK F
Sbjct: 4 YVCTVCGYEYDPAEGDPDNGVKPGTAFEDVPADWVCPICGAPKSEF 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 = 30.4 bits (67), Expect = 0.83, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 11/46 (23%)
Query: 161 HICLDCGYIYFLQ-----------KPFDELPDTYVCPQCQAPKKRF 195
+ C CGYIY + F ++PD +VCP C K +F
Sbjct: 4 YTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGGGKDQF 49
>pdb|1BFY|A Chain A, Solution Structure Of Reduced Clostridium Pasteurianum
Rubredoxin, Nmr, 20 Structures
Length = 54
Score = 30.4 bits (67), Expect = 0.91, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 11/46 (23%)
Query: 161 HICLDCGYIYFLQ-----------KPFDELPDTYVCPQCQAPKKRF 195
+ C CGYIY + F ++PD +VCP C K +F
Sbjct: 4 YTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQF 49
>pdb|1T9Q|A Chain A, Crystal Structure Of V44l Cp Rubredoxin
Length = 54
Score = 30.0 bits (66), Expect = 1.0, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 11/46 (23%)
Query: 161 HICLDCGYIYFLQ-----------KPFDELPDTYVCPQCQAPKKRF 195
+ C CGYIY + F ++PD +VCP C K +F
Sbjct: 4 YTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGLGKDQF 49
>pdb|2EDZ|A Chain A, Solution Structures Of The Pdz Domain Of Mus Musculus Pdz
Domain-Containing Protein 1
Length = 114
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 21/38 (55%)
Query: 63 QKPGGGVVITAVEGGGNAAKAGLKSGDQVLYTSSFFGD 100
+K G +I +E G A KAGL GD+VL + F D
Sbjct: 34 EKDTDGHLIRVIEEGSPAEKAGLLDGDRVLRINGVFVD 71
>pdb|4F8K|A Chain A, Molecular Analysis Of The Interaction Between The
Prostacyclin Receptor And The First Pdz Domain Of Pdzk1
pdb|4F8K|B Chain B, Molecular Analysis Of The Interaction Between The
Prostacyclin Receptor And The First Pdz Domain Of Pdzk1
Length = 109
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 21/38 (55%)
Query: 63 QKPGGGVVITAVEGGGNAAKAGLKSGDQVLYTSSFFGD 100
+K G +I +E G A KAGL GD+VL + F D
Sbjct: 23 EKDTDGHLIRVIEEGSPAEKAGLLDGDRVLRINGVFVD 60
>pdb|3NGH|A Chain A, Molecular Analysis Of The Interaction Of The Hdl Receptor
Sr-Bi With The Adaptor Protein Pdzk1
pdb|3NGH|B Chain B, Molecular Analysis Of The Interaction Of The Hdl Receptor
Sr-Bi With The Adaptor Protein Pdzk1
Length = 106
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 21/38 (55%)
Query: 63 QKPGGGVVITAVEGGGNAAKAGLKSGDQVLYTSSFFGD 100
+K G +I +E G A KAGL GD+VL + F D
Sbjct: 22 EKDTDGHLIRVIEEGSPAEKAGLLDGDRVLRINGVFVD 59
>pdb|1B13|A Chain A, Clostridium Pasteurianum Rubredoxin G10a Mutant
Length = 54
Score = 28.5 bits (62), Expect = 3.2, Method: Composition-based stats.
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 11/46 (23%)
Query: 161 HICLDCGYIYFLQ-----------KPFDELPDTYVCPQCQAPKKRF 195
+ C C YIY + F ++PD +VCP C K +F
Sbjct: 4 YTCTVCAYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQF 49
>pdb|2FUI|A Chain A, Nmr Solution Structure Of Phd Finger Fragment Of Human
Bptf In Free State
pdb|2FUU|A Chain A, Nmr Solution Structure Of The Phd Domain From The Human
Bptf In Complex With H3(1-15)k4me3 Peptide
Length = 62
Score = 28.5 bits (62), Expect = 3.4, Method: Composition-based stats.
Identities = 10/13 (76%), Positives = 11/13 (84%)
Query: 178 ELPDTYVCPQCQA 190
EL D YVCPQCQ+
Sbjct: 46 ELIDEYVCPQCQS 58
>pdb|1F8F|A Chain A, Crystal Structure Of Benzyl Alcohol Dehydrogenase From
Acinetobacter Calcoaceticus
Length = 371
Score = 28.5 bits (62), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 7/60 (11%)
Query: 16 VSDHFLAVSKTKNATRSLDNNKITARTAGASKTIEVEVDKPLGLTLGQKPGGGVVITAVE 75
V+DHF A S S +NN T +K + +E+ PLG G + G G I A++
Sbjct: 135 VNDHFFAQSSFATYALSRENN-----TVKVTKDVPIELLGPLG--CGIQTGAGACINALK 187
>pdb|3MTW|A Chain A, Crystal Structure Of L-Lysine, L-Arginine Carboxypeptidase
Cc2672 From Caulobacter Crescentus Cb15 Complexed With
N-Methyl Phosphonate Derivative Of L-Arginine
Length = 403
Score = 28.1 bits (61), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 17 SDHFLAVSKTKNATRSLDNNKITARTAGASKTIEVEVDKPLGLTLGQKPGGGVVITAVEG 76
SD F +V +T NA ++L+ T R GA+ +V + + + G PG +V A+
Sbjct: 82 SDRFWSVVQTANAKKTLEAGFTTVRNVGAADYDDVGLRE--AIDAGYVPGPRIVTAAISF 139
Query: 77 G 77
G
Sbjct: 140 G 140
>pdb|1QCV|A Chain A, Rubredoxin Variant (Pfrd-Xc4) Folds Without Iron
Length = 53
Score = 27.7 bits (60), Expect = 5.1, Method: Composition-based stats.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 176 FDELPDTYVCPQCQAPKKRFARYD 199
F+ELPD +V P APK F + +
Sbjct: 29 FEELPDDWVAPITGAPKSEFEKLE 52
>pdb|1UEZ|A Chain A, Solution Structure Of The First Pdz Domain Of Human
Kiaa1526 Protein
Length = 101
Score = 27.7 bits (60), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 57 LGLTL--GQKPGGGVVITAVEGGGNAAKAGLKSGDQVL 92
LG ++ G + G G+ ++ VE G A K GL+ GDQ+L
Sbjct: 23 LGFSIRGGSEHGVGIYVSLVEPGSLAEKEGLRVGDQIL 60
>pdb|1B2O|A Chain A, Clostridium Pasteurianum Rubredoxin G10vg43a Mutant
pdb|1B2O|B Chain B, Clostridium Pasteurianum Rubredoxin G10vg43a Mutant
Length = 54
Score = 27.7 bits (60), Expect = 5.4, Method: Composition-based stats.
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 11/46 (23%)
Query: 161 HICLDCGYIYFLQ-----------KPFDELPDTYVCPQCQAPKKRF 195
+ C C YIY + F ++PD +VCP C K +F
Sbjct: 4 YTCTVCVYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCAVGKDQF 49
>pdb|3TSW|A Chain A, Crystal Structure Of The Pdz3-Sh3-Guk Core Module Of
Human Zo-1
pdb|3TSW|C Chain C, Crystal Structure Of The Pdz3-Sh3-Guk Core Module Of
Human Zo-1
pdb|3TSW|D Chain D, Crystal Structure Of The Pdz3-Sh3-Guk Core Module Of
Human Zo-1
pdb|3TSZ|A Chain A, Crystal Structure Of Pdz3-Sh3-Guk Core Module From Human
Zo-1 In Complex With 12mer Peptide From Human Jam-A
Cytoplasmic Tail
Length = 391
Score = 27.3 bits (59), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 57 LGLTLGQKPGGGVVITAVEGGGNAAKAGLKSGDQVLYTSS 96
+GL L G+ + V AAK GL+ GDQ+L ++
Sbjct: 21 VGLRLAGGNDVGIFVAGVLEDSPAAKEGLEEGDQILRVNN 60
>pdb|3SHW|A Chain A, Crystal Structure Of Zo-1 Pdz3-Sh3-Guk Supramodule
Complex With Connexin-45 Peptide
Length = 468
Score = 26.9 bits (58), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 19/36 (52%)
Query: 57 LGLTLGQKPGGGVVITAVEGGGNAAKAGLKSGDQVL 92
+GL L G+ + V AAK GL+ GDQ+L
Sbjct: 13 VGLRLAGGNDVGIFVAGVLEDSPAAKEGLEEGDQIL 48
>pdb|2RI7|A Chain A, Crystal Structure Of Phd Finger-Linker-Bromodomain Y17e
Mutant From Human Bptf In The H3(1-9)k4me2 Bound State
Length = 174
Score = 26.9 bits (58), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 10/13 (76%), Positives = 11/13 (84%)
Query: 178 ELPDTYVCPQCQA 190
EL D YVCPQCQ+
Sbjct: 46 ELIDEYVCPQCQS 58
>pdb|3QZV|A Chain A, Crystal Structure Of Bptf Phd-Linker-Bromo In Complex With
Histone H4k12ac Peptide
Length = 174
Score = 26.9 bits (58), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 10/13 (76%), Positives = 11/13 (84%)
Query: 178 ELPDTYVCPQCQA 190
EL D YVCPQCQ+
Sbjct: 46 ELIDEYVCPQCQS 58
>pdb|4DVY|P Chain P, Crystal Structure Of The Helicobacter Pylori Caga
Oncoprotein
Length = 876
Score = 26.9 bits (58), Expect = 9.4, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 2/52 (3%)
Query: 1 KTTLQGLSLQESKRRVSDHFLAVSKTKNATRSLDNNKITARTAGASKTIEVE 52
K T +GLSLQE+ + + D FL+ +K + A ++L+ NK A EV+
Sbjct: 564 KLTAKGLSLQEANKLIKD-FLSSNK-ELAGKALNFNKAVAEAKSTGNYDEVK 613
>pdb|4G0H|A Chain A, Crystal Structure Of The N-Terminal Domain Of Helicobacter
Pylori Caga Protein
Length = 916
Score = 26.9 bits (58), Expect = 9.8, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 2/52 (3%)
Query: 1 KTTLQGLSLQESKRRVSDHFLAVSKTKNATRSLDNNKITARTAGASKTIEVE 52
K T +GLSLQE+ + + D FL+ +K + A ++L+ NK A EV+
Sbjct: 564 KLTAKGLSLQEANKLIKD-FLSSNK-ELAGKALNFNKAVAEAKSTGNYDEVK 613
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
0.316 0.134 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,111,316
Number of Sequences: 62578
Number of extensions: 256552
Number of successful extensions: 760
Number of sequences better than 100.0: 88
Number of HSP's better than 100.0 without gapping: 61
Number of HSP's successfully gapped in prelim test: 27
Number of HSP's that attempted gapping in prelim test: 682
Number of HSP's gapped (non-prelim): 98
length of query: 235
length of database: 14,973,337
effective HSP length: 96
effective length of query: 139
effective length of database: 8,965,849
effective search space: 1246253011
effective search space used: 1246253011
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)