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= psy4106
(209 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JBV|A Chain A, Crystal Structure Of Choline Oxidase Reveals Insights Into
The Catalytic Mechanism
pdb|2JBV|B Chain B, Crystal Structure Of Choline Oxidase Reveals Insights Into
The Catalytic Mechanism
Length = 546
Score = 84.3 bits (207), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 59/193 (30%), Positives = 98/193 (50%), Gaps = 31/193 (16%)
Query: 18 GWSYDEVRPFFIKSEDNQIENDNIDSLYHRKGGYLTITEIPYKTPIAHAFVQSGYQSGYP 77
GW+ + P + + E N E+ D+ +H G + + +P K P A + + Q+G P
Sbjct: 123 GWNAEAAWPLYKRLETN--EDAGPDAPHHGDSGPVHLMNVPPKDPTGVALLDACEQAGIP 180
Query: 78 IVDVNGAAQTGFSFLPVSFNSARLVMGRAWVQSVEVSMR-NGTRWSTSRAFLHPIRRRRN 136
FN+ V+ A +++ R +GTR S+S +++HPI + N
Sbjct: 181 RA---------------KFNTGTTVVNGA--NFFQINRRADGTRSSSSVSYIHPIVEQEN 223
Query: 137 LHVTKFSLVTKL----IIDEKSKRAVGVELMKG--NSKIRVFARKEVVLSAGAINSPQIL 190
F+L+T L ++ + +R GV+++ R+ AR EVVLS GAI++P++L
Sbjct: 224 -----FTLLTGLRARQLVFDADRRCTGVDIVDSAFGHTHRLTARNEVVLSTGAIDTPKLL 278
Query: 191 MVSGIGPREHLRE 203
M+SGIGP HL E
Sbjct: 279 MLSGIGPAAHLAE 291
>pdb|3LJP|A Chain A, Crystal Structure Of Choline Oxidase V464a Mutant
pdb|3LJP|B Chain B, Crystal Structure Of Choline Oxidase V464a Mutant
Length = 546
Score = 84.3 bits (207), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 59/193 (30%), Positives = 98/193 (50%), Gaps = 31/193 (16%)
Query: 18 GWSYDEVRPFFIKSEDNQIENDNIDSLYHRKGGYLTITEIPYKTPIAHAFVQSGYQSGYP 77
GW+ + P + + E N E+ D+ +H G + + +P K P A + + Q+G P
Sbjct: 123 GWNAEAAWPLYKRLETN--EDAGPDAPHHGDSGPVHLMNVPPKDPTGVALLDACEQAGIP 180
Query: 78 IVDVNGAAQTGFSFLPVSFNSARLVMGRAWVQSVEVSMR-NGTRWSTSRAFLHPIRRRRN 136
FN+ V+ A +++ R +GTR S+S +++HPI + N
Sbjct: 181 RA---------------KFNTGTTVVNGA--NFFQINRRADGTRSSSSVSYIHPIVEQEN 223
Query: 137 LHVTKFSLVTKL----IIDEKSKRAVGVELMKG--NSKIRVFARKEVVLSAGAINSPQIL 190
F+L+T L ++ + +R GV+++ R+ AR EVVLS GAI++P++L
Sbjct: 224 -----FTLLTGLRARQLVFDADRRCTGVDIVDSAFGHTHRLTARNEVVLSTGAIDTPKLL 278
Query: 191 MVSGIGPREHLRE 203
M+SGIGP HL E
Sbjct: 279 MLSGIGPAAHLAE 291
>pdb|3NNE|A Chain A, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|B Chain B, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|C Chain C, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|D Chain D, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|E Chain E, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|F Chain F, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|G Chain G, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|H Chain H, Crystal Structure Of Choline Oxidase S101a Mutant
Length = 546
Score = 84.3 bits (207), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 59/193 (30%), Positives = 98/193 (50%), Gaps = 31/193 (16%)
Query: 18 GWSYDEVRPFFIKSEDNQIENDNIDSLYHRKGGYLTITEIPYKTPIAHAFVQSGYQSGYP 77
GW+ + P + + E N E+ D+ +H G + + +P K P A + + Q+G P
Sbjct: 123 GWNAEAAWPLYKRLETN--EDAGPDAPHHGDSGPVHLMNVPPKDPTGVALLDACEQAGIP 180
Query: 78 IVDVNGAAQTGFSFLPVSFNSARLVMGRAWVQSVEVSMR-NGTRWSTSRAFLHPIRRRRN 136
FN+ V+ A +++ R +GTR S+S +++HPI + N
Sbjct: 181 RA---------------KFNTGTTVVNGA--NFFQINRRADGTRSSSSVSYIHPIVEQEN 223
Query: 137 LHVTKFSLVTKL----IIDEKSKRAVGVELMKG--NSKIRVFARKEVVLSAGAINSPQIL 190
F+L+T L ++ + +R GV+++ R+ AR EVVLS GAI++P++L
Sbjct: 224 -----FTLLTGLRARQLVFDADRRCTGVDIVDSAFGHTHRLTARNEVVLSTGAIDTPKLL 278
Query: 191 MVSGIGPREHLRE 203
M+SGIGP HL E
Sbjct: 279 MLSGIGPAAHLAE 291
>pdb|3T37|A Chain A, Crystal Structure Of Pyridoxine 4-Oxidase From Mesorbium
Loti
Length = 526
Score = 66.2 bits (160), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 57/194 (29%), Positives = 97/194 (50%), Gaps = 28/194 (14%)
Query: 12 AYVEGPG---WSYDEVRPFFIKSEDNQIENDNIDSLYHRKGGYLTITEIPYKTPIAHAFV 68
A+V+ G W +DE+ P F ED+ + D I +L E+ +P+A AF+
Sbjct: 118 AWVDASGDRRWGWDELLPVFQAIEDHPLGGDGIHGKGGPLPIHLPADEV---SPLARAFI 174
Query: 69 QSGYQSGYPIVDVNGAAQTGFSFLPVSFNSARLVMGRAWVQSVEVSMRNGTRWSTSRAFL 128
++G G P ++ + + + P S N +R+G R + + A+L
Sbjct: 175 EAGASLGLPRLEGHNSGEM-IGVTPNSLN-----------------IRDGRRVTAADAWL 216
Query: 129 -HPIRRRRNLHVTKFSLVTKLIIDEKSKRAVGVELMKGNSKIRVFARKEVVLSAGAINSP 187
+R R+NL + S V +L ++ R++ V +G+++ VFA ++VL AGA+ SP
Sbjct: 217 TKAVRGRKNLTILTGSRVRRLKLEGNQVRSLEVVGRQGSAE--VFA-DQIVLCAGALESP 273
Query: 188 QILMVSGIGPREHL 201
+LM SGIGP + L
Sbjct: 274 ALLMRSGIGPHDVL 287
>pdb|3FIM|B Chain B, Crystal Structure Of Aryl-Alcohol-Oxidase From Pleurotus
Eryingii
Length = 566
Score = 63.2 bits (152), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 57/206 (27%), Positives = 89/206 (43%), Gaps = 27/206 (13%)
Query: 7 FRQTVAYVEGPGWSYDEVRPFFIKSE------DNQIENDNIDSLYHRKGGYLTITEIPYK 60
F + A GW++D ++ F K+E DN + H G ++I+ +
Sbjct: 103 FDRYAAVTGDEGWNWDNIQQFVRKNEMVVPPADNHNTSGEFIPAVHGTNGSVSISLPGFP 162
Query: 61 TPIAHAFVQSGYQSGYPIVDVNGAAQTGFSFLPVSFNSARLVMGRAWVQSVEVSMRNGTR 120
TP+ + + + N TG +G +W + S+ NG R
Sbjct: 163 TPLDDRVLATTQEQSEEFF-FNPDMGTGHP------------LGISWSIA---SVGNGQR 206
Query: 121 WSTSRAFLHPIRRRRNLHVTKFSLVTKLIIDEKSK-----RAVGVELMKGNSKIRVFARK 175
S+S A+L P + R NL V + VTKL+ + R V +G V A+K
Sbjct: 207 SSSSTAYLRPAQSRPNLSVLINAQVTKLVNSGTTNGLPAFRCVEYAEQEGAPTTTVCAKK 266
Query: 176 EVVLSAGAINSPQILMVSGIGPREHL 201
EVVLSAG++ +P +L +SGIG L
Sbjct: 267 EVVLSAGSVGTPILLQLSGIGDENDL 292
>pdb|1CF3|A Chain A, Glucose Oxidase From Apergillus Niger
pdb|1GAL|A Chain A, Crystal Structure Of Glucose Oxidase From Aspergillus
Niger: Refined At 2.3 Angstroms Resolution
pdb|3QVP|A Chain A, Crystal Structure Of Glucose Oxidase For Space Group C2221
At 1.2 A Resolution
pdb|3QVR|A Chain A, Crystal Structure Of Glucose Oxidase For Space Group P3121
At 1.3 A Resolution
Length = 583
Score = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 35/87 (40%), Positives = 50/87 (57%), Gaps = 5/87 (5%)
Query: 120 RWSTSRAFLHPIRRRRNLHVTKFSLVTKLIIDEK--SKRAVGVEL--MKGNSKIRVFARK 175
R +R +L P +R NL V V K+++ + + RAVGVE KGN+ V+A+
Sbjct: 225 RSDAAREWLLPNYQRPNLQVLTGQYVGKVLLSQNGTTPRAVGVEFGTHKGNTH-NVYAKH 283
Query: 176 EVVLSAGAINSPQILMVSGIGPREHLR 202
EV+L+AG+ SP IL SGIG + L
Sbjct: 284 EVLLAAGSAVSPTILEYSGIGMKSILE 310
>pdb|1GPE|A Chain A, Glucose Oxidase From Penicillium Amagasakiense
pdb|1GPE|B Chain B, Glucose Oxidase From Penicillium Amagasakiense
Length = 587
Score = 50.1 bits (118), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 32/93 (34%), Positives = 50/93 (53%), Gaps = 3/93 (3%)
Query: 116 RNGTRWSTSRAFLHPIRRRRNLHVTKFSLVTKLIIDEKSK--RAVGVELMKGNS-KIRVF 172
N R +RA+L P +R NL + +V K++ + + +AVGV + VF
Sbjct: 225 ENQVRVDAARAWLLPNYQRSNLEILTGQMVGKVLFKQTASGPQAVGVNFGTNKAVNFDVF 284
Query: 173 ARKEVVLSAGAINSPQILMVSGIGPREHLREKS 205
A+ EV+L+AG+ SP IL SGIG + L + +
Sbjct: 285 AKHEVLLAAGSAISPLILEYSGIGLKSVLDQAN 317
>pdb|3Q9T|A Chain A, Crystal Structure Analysis Of Formate Oxidase
pdb|3Q9T|B Chain B, Crystal Structure Analysis Of Formate Oxidase
pdb|3Q9T|C Chain C, Crystal Structure Analysis Of Formate Oxidase
Length = 577
Score = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 47/83 (56%), Gaps = 2/83 (2%)
Query: 120 RWSTSRAFLHPIRRRRNLHVTKFSLVTKLIIDEKSKRAVGVELMKG-NSKIRVFARKEVV 178
R S +FL ++ + N+ + +LII+E + GV ++ +++ FA +EV+
Sbjct: 205 RGQRSGSFLF-VKNKPNITIVPEVHSKRLIINEADRTCKGVTVVTAAGNELNFFADREVI 263
Query: 179 LSAGAINSPQILMVSGIGPREHL 201
LS G +P++LM+SGIGP L
Sbjct: 264 LSQGVFETPKLLMLSGIGPTREL 286
>pdb|3RED|A Chain A, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|B Chain B, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|C Chain C, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|D Chain D, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|E Chain E, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|F Chain F, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|G Chain G, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|H Chain H, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|I Chain I, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|J Chain J, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|K Chain K, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|L Chain L, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
Length = 521
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 33/91 (36%), Positives = 47/91 (51%), Gaps = 7/91 (7%)
Query: 116 RNGTRWSTSRAFLHPIRRRRNLHVTKFSLVTKLIIDEKSK--RAVGVELMKGN-SKIRVF 172
NGTR ++ L NL V + V K+I S A+GV N + + F
Sbjct: 190 NNGTRHASDE--LLNKGDPNNLRVAVHASVEKIIFSSNSSGVTAIGVIYKDSNGTPHQAF 247
Query: 173 ARKE--VVLSAGAINSPQILMVSGIGPREHL 201
R E V++SAG I SPQ+L++SG+GP +L
Sbjct: 248 VRGEGEVIVSAGPIGSPQLLLLSGVGPESYL 278
>pdb|3GDN|A Chain A, Almond Hydroxynitrile Lyase In Complex With Benzaldehyde
pdb|3GDN|B Chain B, Almond Hydroxynitrile Lyase In Complex With Benzaldehyde
pdb|3GDP|A Chain A, Hydroxynitrile Lyase From Almond, Monoclinic Crystal Form
pdb|3GDP|B Chain B, Hydroxynitrile Lyase From Almond, Monoclinic Crystal Form
Length = 521
Score = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 135 RNLHVTKFSLVTKLII-DEKSKRAVGVELMKGNS---KIRVFARKEVVLSAGAINSPQIL 190
NL V + V K+I + A GV N + V ++ EV++SAG I +PQ+L
Sbjct: 207 NNLRVGVHASVEKIIFSNAPGLTATGVIYRDSNGTPHQAFVRSKGEVIVSAGTIGTPQLL 266
Query: 191 MVSGIGPREHL 201
++SG+GP +L
Sbjct: 267 LLSGVGPESYL 277
>pdb|1JU2|A Chain A, Crystal Structure Of The Hydroxynitrile Lyase From Almond
pdb|1JU2|B Chain B, Crystal Structure Of The Hydroxynitrile Lyase From Almond
Length = 536
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 135 RNLHVTKFSLVTKLII-DEKSKRAVGVELMKGNS---KIRVFARKEVVLSAGAINSPQIL 190
NL V + V K+I + A GV N + V ++ EV++SAG I +PQ+L
Sbjct: 207 NNLRVGVHASVEKIIFSNAPGLTATGVIYRDSNGTPHQAFVRSKGEVIVSAGTIGTPQLL 266
Query: 191 MVSGIGPREHL 201
++SG+GP +L
Sbjct: 267 LLSGVGPESYL 277
>pdb|1NAA|A Chain A, Cellobiose Dehydrogenase Flavoprotein Fragment In Complex
With Cellobionolactam
pdb|1NAA|B Chain B, Cellobiose Dehydrogenase Flavoprotein Fragment In Complex
With Cellobionolactam
Length = 541
Score = 35.4 bits (80), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 41/90 (45%), Gaps = 6/90 (6%)
Query: 117 NGTRWSTSRAFLHPIRRRRNLHVTKFSLVTKLIIDEKSKRAVGVEL----MKGNSKIRVF 172
NG R +L R N +V+ ++ + +GV+ + N I V
Sbjct: 186 NGKRAGPVATYLQTALARPNFTFKTNVMVSNVV--RNGSQILGVQTNDPTLGPNGFIPVT 243
Query: 173 ARKEVVLSAGAINSPQILMVSGIGPREHLR 202
+ V+LSAGA + +IL SGIGP + ++
Sbjct: 244 PKGRVILSAGAFGTSRILFQSGIGPTDMIQ 273
>pdb|1KDG|A Chain A, Crystal Structure Of The Flavin Domain Of Cellobiose
Dehydrogenase
pdb|1KDG|B Chain B, Crystal Structure Of The Flavin Domain Of Cellobiose
Dehydrogenase
Length = 546
Score = 35.4 bits (80), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 41/90 (45%), Gaps = 6/90 (6%)
Query: 117 NGTRWSTSRAFLHPIRRRRNLHVTKFSLVTKLIIDEKSKRAVGVEL----MKGNSKIRVF 172
NG R +L R N +V+ ++ + +GV+ + N I V
Sbjct: 191 NGKRAGPVATYLQTALARPNFTFKTNVMVSNVV--RNGSQILGVQTNDPTLGPNGFIPVT 248
Query: 173 ARKEVVLSAGAINSPQILMVSGIGPREHLR 202
+ V+LSAGA + +IL SGIGP + ++
Sbjct: 249 PKGRVILSAGAFGTSRILFQSGIGPTDMIQ 278
>pdb|3D3Q|A Chain A, Crystal Structure Of Trna
Delta(2)-Isopentenylpyrophosphate Transferase (Se0981)
From Staphylococcus Epidermidis. Northeast Structural
Genomics Consortium Target Ser100
pdb|3D3Q|B Chain B, Crystal Structure Of Trna
Delta(2)-Isopentenylpyrophosphate Transferase (Se0981)
From Staphylococcus Epidermidis. Northeast Structural
Genomics Consortium Target Ser100
Length = 340
Score = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 10/77 (12%)
Query: 128 LHPIRRRRNLHVTKFSLVTKLIIDEKSK----------RAVGVELMKGNSKIRVFARKEV 177
+HP R+R L ++ L TK ++ + K +G+E + +R+ R ++
Sbjct: 161 IHPNNRKRVLRAIEYYLKTKKLLSSRKKVQQFTENYDTLLIGIEXSRETLYLRINKRVDI 220
Query: 178 VLSAGAINSPQILMVSG 194
L G N Q L+ G
Sbjct: 221 XLGHGLFNEVQHLVEQG 237
>pdb|3KKZ|A Chain A, Crystal Structure Of The Q5les9_bacfn Protein From
Bacteroides Fragilis. Northeast Structural Genomics
Consortium Target Bfr250.
pdb|3KKZ|B Chain B, Crystal Structure Of The Q5les9_bacfn Protein From
Bacteroides Fragilis. Northeast Structural Genomics
Consortium Target Bfr250
Length = 267
Score = 28.1 bits (61), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 19/37 (51%)
Query: 45 YHRKGGYLTITEIPYKTPIAHAFVQSGYQSGYPIVDV 81
Y +KGGYL ++E + T A + + YP +D
Sbjct: 139 YLKKGGYLAVSECSWFTDERPAEINDFWXDAYPEIDT 175
>pdb|4GRI|A Chain A, Crystal Structure Of A Glutamyl-Trna Synthetase Glurs From
Borrelia Burgdorferi Bound To Glutamic Acid And Zinc
pdb|4GRI|B Chain B, Crystal Structure Of A Glutamyl-Trna Synthetase Glurs From
Borrelia Burgdorferi Bound To Glutamic Acid And Zinc
Length = 512
Score = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 11 VAYVEGPGWSYDEVRPFFIKSEDNQ 35
+ YV GWSYD+ R FF K++ Q
Sbjct: 297 INYVTLLGWSYDDKREFFSKNDLEQ 321
>pdb|2L8B|A Chain A, Trai (381-569)
Length = 189
Score = 26.9 bits (58), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 9/64 (14%)
Query: 149 IIDEKSKRAVGVELMKGNSKIRVFARKEVVLSAG--------AINSPQILMVSGIGPREH 200
++DE S RA+ ++MK N ++ V K V +AG A + P + +VSG G
Sbjct: 6 VLDELSVRALSRDIMKQN-RVTVHPEKSVPRTAGYSDAVSVLAQDRPSLAIVSGQGGAAG 64
Query: 201 LREK 204
RE+
Sbjct: 65 QRER 68
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 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,070,677
Number of Sequences: 62578
Number of extensions: 232682
Number of successful extensions: 467
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 442
Number of HSP's gapped (non-prelim): 17
length of query: 209
length of database: 14,973,337
effective HSP length: 94
effective length of query: 115
effective length of database: 9,091,005
effective search space: 1045465575
effective search space used: 1045465575
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: 49 (23.5 bits)