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= 039983
(220 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2A33|A Chain A, X-Ray Structure Of A Lysine Decarboxylase-Like Protein
From Arabidopsis Thaliana Gene At2g37210
pdb|2A33|B Chain B, X-Ray Structure Of A Lysine Decarboxylase-Like Protein
From Arabidopsis Thaliana Gene At2g37210
pdb|2Q4O|A Chain A, Ensemble Refinement Of The Crystal Structure Of A Lysine
Decarboxylase-Like Protein From Arabidopsis Thaliana
Gene At2g37210
pdb|2Q4O|B Chain B, Ensemble Refinement Of The Crystal Structure Of A Lysine
Decarboxylase-Like Protein From Arabidopsis Thaliana
Gene At2g37210
Length = 215
Score = 255 bits (651), Expect = 1e-68, Method: Compositional matrix adjust.
Identities = 128/189 (67%), Positives = 158/189 (83%)
Query: 8 KSRFKRVCVFCGSSPDYKYCYRKAAVDLGNELVSRGLDLVYGGGSVGLMGLISEEVHRGG 67
KS+F+R+CVFCGSS K Y+ AAVDLGNELVSR +DLVYGGGS+GL GL+S+ VH GG
Sbjct: 10 KSKFRRICVFCGSSQGKKSSYQDAAVDLGNELVSRNIDLVYGGGSIGLXGLVSQAVHDGG 69
Query: 68 RHVLGIIPKALMKKELTGVTLGEVKPVDHMHQRKAEMARNADCFIALPGGFGTLEELFEV 127
RHV+GIIPK L +ELTG T+GEV+ V HQRKAE A+++D FIALPGG+GTLEEL EV
Sbjct: 70 RHVIGIIPKTLXPRELTGETVGEVRAVADXHQRKAEXAKHSDAFIALPGGYGTLEELLEV 129
Query: 128 TTWSQLGIHNKPVGLINVEGYYDPILNFIDKSIDEGFIYPSQRSIIVSASNAKELVQKLE 187
TW+QLGIH+KPVGL+NV+GYY+ +L+FIDK+++EGFI P+ R IIVSA AKELV+KLE
Sbjct: 130 ITWAQLGIHDKPVGLLNVDGYYNSLLSFIDKAVEEGFISPTAREIIVSAPTAKELVKKLE 189
Query: 188 DYVPSHDGV 196
+Y P H+ V
Sbjct: 190 EYAPCHERV 198
>pdb|1YDH|A Chain A, X-Ray Structure Of A Lysine Decarboxylase-Like Protein
From Arabidopsis Thaliana Gene At5g11950
pdb|1YDH|B Chain B, X-Ray Structure Of A Lysine Decarboxylase-Like Protein
From Arabidopsis Thaliana Gene At5g11950
pdb|2Q4D|A Chain A, Ensemble Refinement Of The Crystal Structure Of A Lysine
Decarboxylase-Like Protein From Arabidopsis Thaliana
Gene At5g11950
pdb|2Q4D|B Chain B, Ensemble Refinement Of The Crystal Structure Of A Lysine
Decarboxylase-Like Protein From Arabidopsis Thaliana
Gene At5g11950
Length = 216
Score = 190 bits (483), Expect = 5e-49, Method: Compositional matrix adjust.
Identities = 111/189 (58%), Positives = 141/189 (74%)
Query: 8 KSRFKRVCVFCGSSPDYKYCYRKAAVDLGNELVSRGLDLVYGGGSVGLMGLISEEVHRGG 67
+SRF+++CVFCGS ++ + AA++LGNELV R +DLVYGGGSVGL GLIS V+ GG
Sbjct: 6 RSRFRKICVFCGSHSGHREVFSDAAIELGNELVKRKIDLVYGGGSVGLXGLISRRVYEGG 65
Query: 68 RHVLGIIPKALMKKELTGVTLGEVKPVDHMHQRKAEMARNADCFIALPGGFGTLEELFEV 127
HVLGIIPKAL E++G T+G+V+ V H+RKA A+ A+ FIALPGG+GT EEL E
Sbjct: 66 LHVLGIIPKALXPIEISGETVGDVRVVADXHERKAAXAQEAEAFIALPGGYGTXEELLEX 125
Query: 128 TTWSQLGIHNKPVGLINVEGYYDPILNFIDKSIDEGFIYPSQRSIIVSASNAKELVQKLE 187
TWSQLGIH K VGL+NV+GYY+ +L D ++EGFI P R+I+VSA AKEL +K E
Sbjct: 126 ITWSQLGIHKKTVGLLNVDGYYNNLLALFDTGVEEGFIKPGARNIVVSAPTAKELXEKXE 185
Query: 188 DYVPSHDGV 196
+Y PSH V
Sbjct: 186 EYTPSHXHV 194
>pdb|1T35|A Chain A, Crystal Structure Of A Hypothetical Protein Yvdd- A
Putative Lysine Decarboxylase
pdb|1T35|B Chain B, Crystal Structure Of A Hypothetical Protein Yvdd- A
Putative Lysine Decarboxylase
pdb|1T35|C Chain C, Crystal Structure Of A Hypothetical Protein Yvdd- A
Putative Lysine Decarboxylase
pdb|1T35|D Chain D, Crystal Structure Of A Hypothetical Protein Yvdd- A
Putative Lysine Decarboxylase
pdb|1T35|E Chain E, Crystal Structure Of A Hypothetical Protein Yvdd- A
Putative Lysine Decarboxylase
pdb|1T35|F Chain F, Crystal Structure Of A Hypothetical Protein Yvdd- A
Putative Lysine Decarboxylase
pdb|1T35|G Chain G, Crystal Structure Of A Hypothetical Protein Yvdd- A
Putative Lysine Decarboxylase
pdb|1T35|H Chain H, Crystal Structure Of A Hypothetical Protein Yvdd- A
Putative Lysine Decarboxylase
Length = 191
Score = 156 bits (394), Expect = 8e-39, Method: Compositional matrix adjust.
Identities = 76/178 (42%), Positives = 108/178 (60%)
Query: 12 KRVCVFCGSSPDYKYCYRKAAVDLGNELVSRGLDLVYGGGSVGLMGLISEEVHRGGRHVL 71
K +CVF GS+P Y++ A +LG +G+ LVYGG VGL G I++ + G +
Sbjct: 2 KTICVFAGSNPGGNEAYKRKAAELGVYXAEQGIGLVYGGSRVGLXGTIADAIXENGGTAI 61
Query: 72 GIIPKALMKKELTGVTLGEVKPVDHMHQRKAEMARNADCFIALPGGFGTLEELFEVTTWS 131
G+ P L E+ L E+ V+ H+RKA+ + AD FI+ PGGFGT EELFEV W+
Sbjct: 62 GVXPSGLFSGEVVHQNLTELIEVNGXHERKAKXSELADGFISXPGGFGTYEELFEVLCWA 121
Query: 132 QLGIHNKPVGLINVEGYYDPILNFIDKSIDEGFIYPSQRSIIVSASNAKELVQKLEDY 189
Q+GIH KP+GL NV GY++P + SI EGF S +I S+S EL+++ ++Y
Sbjct: 122 QIGIHQKPIGLYNVNGYFEPXXKXVKYSIQEGFSNESHLKLIHSSSRPDELIEQXQNY 179
>pdb|3QUA|A Chain A, Crystal Structure Of A Putative Uncharacterized Protein
And Possible Molybdenum Cofactor Protein From
Mycobacterium Smegmatis
pdb|3QUA|B Chain B, Crystal Structure Of A Putative Uncharacterized Protein
And Possible Molybdenum Cofactor Protein From
Mycobacterium Smegmatis
Length = 199
Score = 136 bits (342), Expect = 9e-33, Method: Compositional matrix adjust.
Identities = 70/168 (41%), Positives = 103/168 (61%), Gaps = 3/168 (1%)
Query: 5 KEAKSRFKRVCVFCGSSPDYKYCYRKAAVDLGNELVSRGLDLVYGGGSVGLMGLISEEVH 64
KE + R VCV+C S P + AA ++G+ + +RG LV GGG+V MG +++
Sbjct: 16 KEGQDRQWAVCVYCASGPTHPELLELAA-EVGSSIAARGWTLVSGGGNVSAMGAVAQAAR 74
Query: 65 RGGRHVLGIIPKALMKKELTGVTLGEVKPVDHMHQRKAEMARNADCFIALPGGFGTLEEL 124
G H +G+IPKAL+ +EL V E+ D M +RK EM +D FIALPGG GTLEE
Sbjct: 75 AKGGHTVGVIPKALVHRELADVDAAELIVTDTMRERKREMEHRSDAFIALPGGIGTLEEF 134
Query: 125 FEVTTWSQLGIHNKPVGLINVEGYYDPILNFIDKSIDEGFIYPSQRSI 172
FE T LG+H+KP+ L++ G+YD +L ++ + G++ SQR++
Sbjct: 135 FEAWTAGYLGMHDKPLILLDPFGHYDGLLTWLRGLVPTGYV--SQRAM 180
>pdb|3SBX|A Chain A, Crystal Structure Of A Putative Uncharacterized Protein
From Mycobacterium Marinum Bound To Adenosine
5'-Monophosphate Amp
pdb|3SBX|B Chain B, Crystal Structure Of A Putative Uncharacterized Protein
From Mycobacterium Marinum Bound To Adenosine
5'-Monophosphate Amp
pdb|3SBX|C Chain C, Crystal Structure Of A Putative Uncharacterized Protein
From Mycobacterium Marinum Bound To Adenosine
5'-Monophosphate Amp
pdb|3SBX|D Chain D, Crystal Structure Of A Putative Uncharacterized Protein
From Mycobacterium Marinum Bound To Adenosine
5'-Monophosphate Amp
pdb|3SBX|E Chain E, Crystal Structure Of A Putative Uncharacterized Protein
From Mycobacterium Marinum Bound To Adenosine
5'-Monophosphate Amp
pdb|3SBX|F Chain F, Crystal Structure Of A Putative Uncharacterized Protein
From Mycobacterium Marinum Bound To Adenosine
5'-Monophosphate Amp
pdb|3SBX|G Chain G, Crystal Structure Of A Putative Uncharacterized Protein
From Mycobacterium Marinum Bound To Adenosine
5'-Monophosphate Amp
pdb|3SBX|H Chain H, Crystal Structure Of A Putative Uncharacterized Protein
From Mycobacterium Marinum Bound To Adenosine
5'-Monophosphate Amp
Length = 189
Score = 90.9 bits (224), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 56/181 (30%), Positives = 97/181 (53%), Gaps = 2/181 (1%)
Query: 4 KKEAKSRFKRVCVFCGSSPDYKYCYRKAAVDLGNELVSRGLDLVYGGGSVGLMGLISEEV 63
K + R+ V V+C ++P + + A +G + +RG LV+GGG V MG +S
Sbjct: 7 KSDEPGRWT-VAVYCAAAPTHPELL-ELAGAVGAAIAARGWTLVWGGGHVSAMGAVSSAA 64
Query: 64 HRGGRHVLGIIPKALMKKELTGVTLGEVKPVDHMHQRKAEMARNADCFIALPGGFGTLEE 123
G +G+IPK L+ +EL E+ + M +RK M A+ FI LPGG GTL+E
Sbjct: 65 RAHGGWTVGVIPKMLVHRELADHDADELVVTETMWERKQVMEDRANAFITLPGGVGTLDE 124
Query: 124 LFEVTTWSQLGIHNKPVGLINVEGYYDPILNFIDKSIDEGFIYPSQRSIIVSASNAKELV 183
L +V T LG+H+K + +++ G++D + ++ + D G++ + ++ N + +
Sbjct: 125 LLDVWTEGYLGMHDKSIVVLDPWGHFDGLRAWLSELADTGYVSRTAMERLIVVDNLDDAL 184
Query: 184 Q 184
Q
Sbjct: 185 Q 185
>pdb|1WEK|A Chain A, Crystal Structure Of The Conserved Hypothetical Protein
Tt1465 From Thermus Thermophilus Hb8
pdb|1WEK|B Chain B, Crystal Structure Of The Conserved Hypothetical Protein
Tt1465 From Thermus Thermophilus Hb8
pdb|1WEK|C Chain C, Crystal Structure Of The Conserved Hypothetical Protein
Tt1465 From Thermus Thermophilus Hb8
pdb|1WEK|D Chain D, Crystal Structure Of The Conserved Hypothetical Protein
Tt1465 From Thermus Thermophilus Hb8
pdb|1WEK|E Chain E, Crystal Structure Of The Conserved Hypothetical Protein
Tt1465 From Thermus Thermophilus Hb8
pdb|1WEK|F Chain F, Crystal Structure Of The Conserved Hypothetical Protein
Tt1465 From Thermus Thermophilus Hb8
Length = 217
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 31/93 (33%), Positives = 48/93 (51%), Gaps = 2/93 (2%)
Query: 100 RKAEMARNADCFIALPGGFGTLEELFEVTTWSQL-GIHNKPVGLINVEGYYDPILNFIDK 158
RK R A F+ LPGGFGTL+EL EV Q +H PV L++ GY++ ++ ++
Sbjct: 124 RKVLFVRYAVGFVFLPGGFGTLDELSEVLVLLQTEKVHRFPVFLLD-RGYWEGLVRWLAF 182
Query: 159 SIDEGFIYPSQRSIIVSASNAKELVQKLEDYVP 191
D+ + P + +E+VQ L+ P
Sbjct: 183 LRDQKAVGPEDLQLFRLTDEPEEVVQALKAEAP 215
>pdb|1RCU|A Chain A, X-Ray Structure Of Tm1055 Northeast Structural Genomics
Consortium Target Vt76
pdb|1RCU|B Chain B, X-Ray Structure Of Tm1055 Northeast Structural Genomics
Consortium Target Vt76
pdb|1RCU|C Chain C, X-Ray Structure Of Tm1055 Northeast Structural Genomics
Consortium Target Vt76
pdb|1RCU|D Chain D, X-Ray Structure Of Tm1055 Northeast Structural Genomics
Consortium Target Vt76
Length = 195
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 53/185 (28%), Positives = 80/185 (43%), Gaps = 17/185 (9%)
Query: 12 KRVCVFCGSSPDYKYC---YRKAAVDLGNELVSRGLDLVYGGGSVGLMGLISEEVHRGGR 68
K+V V S P K R ++LG L +G LV+ GG G+ L+S+ V G
Sbjct: 24 KKVVVVGYSGPVNKSPVSELRDICLELGRTLAKKGY-LVFNGGRDGVXELVSQGVREAGG 82
Query: 69 HVLGIIPKALMKKELTGVTLGEVKPVDHMHQRKAEMARNADCFIALPGGFGTLEELFEVT 128
V+GI+P V VK R + RNAD +++ G GT E+
Sbjct: 83 TVVGILPDEEAGNPYLSVA---VKTGLDFQXRSFVLLRNADVVVSIGGEIGTAIEILGAY 139
Query: 129 TWSQLGIHNKPVGLINVEGYYDPILNFIDKSIDEGFIYPSQRSI-IVSASNAKELVQKLE 187
LG KPV L+ G + + I + + +G ++R + I A +E VQ +E
Sbjct: 140 A---LG---KPVILLRGTGGWT---DRISQVLIDGKYLDNRRIVEIHQAWTVEEAVQIIE 190
Query: 188 DYVPS 192
+ S
Sbjct: 191 QILGS 195
>pdb|3BQ9|A Chain A, Crystal Structure Of Predicted Nucleotide-Binding Protein
From Idiomarina Baltica Os145
pdb|3BQ9|B Chain B, Crystal Structure Of Predicted Nucleotide-Binding Protein
From Idiomarina Baltica Os145
Length = 460
Score = 35.0 bits (79), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 32/119 (26%), Positives = 53/119 (44%), Gaps = 11/119 (9%)
Query: 14 VCVFCGSSPDYKYCYRKAAVDLGNELVSRGLDLVYGGGSVGLMGLI-------SEEVHRG 66
VC S + +Y Y K D+G + RGL++ G G + G + +++ G
Sbjct: 149 VCWGGHSINEIEYKYTK---DVGYHIGLRGLNICTGCGPGAMKGPMKGATIGHAKQRVEG 205
Query: 67 GRHVLGIIPKALMKKELTGVTLGEVKPVDHMHQRKAEMARNADCFIALPGGFGTLEELF 125
GR+ LG+ ++ E + E+ + + +R R A + PGG GT EEL
Sbjct: 206 GRY-LGLTEPGIIAAEPPNPIVNELVILPDIEKRLEAFVRCAHGIVIFPGGAGTAEELL 263
>pdb|2PMB|A Chain A, Crystal Structure Of Predicted Nucleotide-binding Protein
From Vibrio Cholerae
pdb|2PMB|B Chain B, Crystal Structure Of Predicted Nucleotide-binding Protein
From Vibrio Cholerae
pdb|2PMB|C Chain C, Crystal Structure Of Predicted Nucleotide-binding Protein
From Vibrio Cholerae
pdb|2PMB|D Chain D, Crystal Structure Of Predicted Nucleotide-binding Protein
From Vibrio Cholerae
pdb|3GH1|A Chain A, Crystal Structure Of Predicted Nucleotide-Binding Protein
From Vibrio Cholerae
pdb|3GH1|B Chain B, Crystal Structure Of Predicted Nucleotide-Binding Protein
From Vibrio Cholerae
pdb|3GH1|C Chain C, Crystal Structure Of Predicted Nucleotide-Binding Protein
From Vibrio Cholerae
pdb|3GH1|D Chain D, Crystal Structure Of Predicted Nucleotide-Binding Protein
From Vibrio Cholerae
Length = 462
Score = 30.8 bits (68), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 41/167 (24%), Positives = 63/167 (37%), Gaps = 25/167 (14%)
Query: 14 VCVFCGSSPDYKYCYRKAAVDLGNELVSRGLDLVYGGGSVGLMGLISEEV--HRGGRH-- 69
VC S + +Y Y + ++G+EL R L++ G G G H R+
Sbjct: 151 VCWGGHSINEVEYQYTR---EVGHELGLRELNICTGCGPGAXEGPXKGAAVGHAKQRYSE 207
Query: 70 --VLGIIPKALMKKELTGVTLGEVKPVDHMHQRKAEMARNADCFIALPGGFGTLEELFEV 127
LG+ +++ E + E+ + +R R A I PGG GT EEL +
Sbjct: 208 YRYLGLTEPSIIAAEPPNPIVNELVIXPDIEKRLEAFVRXAHGIIIFPGGPGTAEELLYI 267
Query: 128 TTWSQLGIHNKP-----------VGLINVEGYYDPILNFIDKSIDEG 163
LGI P G E Y+ + FI ++ E
Sbjct: 268 -----LGIXXHPENADQPXPIVLTGPKQSEAYFRSLDKFITDTLGEA 309
>pdb|1WEH|A Chain A, Crystal Structure Of The Conserved Hypothetical Protein
Tt1887 From Thermus Thermophilus Hb8
pdb|1WEH|B Chain B, Crystal Structure Of The Conserved Hypothetical Protein
Tt1887 From Thermus Thermophilus Hb8
Length = 171
Score = 30.0 bits (66), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 93 PVDHMHQRKAEMARNADCFIALPGGFGTLEELFEVTTWSQL 133
P + QR + ++ALPGG GTL EL V W+ L
Sbjct: 83 PAATLPQRIGRLLDLGAGYLALPGGVGTLAEL--VLAWNLL 121
>pdb|1V5F|A Chain A, Crystal Structure Of Pyruvate Oxidase Complexed With Fad
And Tpp, From Aerococcus Viridans
pdb|1V5G|A Chain A, Crystal Structure Of The Reaction Intermediate Between
Pyruvate Oxidase Containing Fad And Tpp, And Substrate
Pyruvate
Length = 589
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 9/80 (11%)
Query: 94 VDHMHQRKAEMARNADCF----IALPGGFGTLEELFEVTTWSQLG----IHNKPVGLINV 145
+ H+H M R + F IA+PGG G + W+ +G P + NV
Sbjct: 394 IRHLHMTPKNMWRTSPLFATMGIAIPGGLGAKNTYPDRQVWNIIGDGAFSMTYPDVVTNV 453
Query: 146 EGYYDPILNFIDKSIDEGFI 165
Y P++N + + + FI
Sbjct: 454 R-YNMPVINVVFSNTEYAFI 472
>pdb|1V5E|A Chain A, Crystal Structure Of Pyruvate Oxidase Containing Fad, From
Aerococcus Viridans
pdb|2DJI|A Chain A, Crystal Structure Of Pyruvate Oxidase From Aerococcus
Viridans Containing Fad
Length = 590
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 9/80 (11%)
Query: 94 VDHMHQRKAEMARNADCF----IALPGGFGTLEELFEVTTWSQLG----IHNKPVGLINV 145
+ H+H M R + F IA+PGG G + W+ +G P + NV
Sbjct: 395 IRHLHMTPKNMWRTSPLFATMGIAIPGGLGAKNTYPDRQVWNIIGDGAFSMTYPDVVTNV 454
Query: 146 EGYYDPILNFIDKSIDEGFI 165
Y P++N + + + FI
Sbjct: 455 R-YNMPVINVVFSNTEYAFI 473
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
0.317 0.138 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,565,742
Number of Sequences: 62578
Number of extensions: 283256
Number of successful extensions: 583
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 568
Number of HSP's gapped (non-prelim): 17
length of query: 220
length of database: 14,973,337
effective HSP length: 95
effective length of query: 125
effective length of database: 9,028,427
effective search space: 1128553375
effective search space used: 1128553375
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: 49 (23.5 bits)