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= 046181
(234 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1PXZ|A Chain A, 1.7 Angstrom Crystal Structure Of Jun A 1, The Major
Allergen From Cedar Pollen
pdb|1PXZ|B Chain B, 1.7 Angstrom Crystal Structure Of Jun A 1, The Major
Allergen From Cedar Pollen
Length = 346
Score = 89.0 bits (219), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 54/133 (40%), Positives = 66/133 (49%), Gaps = 27/133 (20%)
Query: 115 AIRLVTTSKVWIDHNIRYECQDGLIDVRRGSTDVTISNNWFRNQEK------------RQ 162
AI + + WIDHN +C DGLIDV GST +TISNN F N K +
Sbjct: 152 AITMRNVTNAWIDHNSLSDCSDGLIDVTLGSTGITISNNHFFNHHKVMLLGHDDTYDDDK 211
Query: 163 NMKVIVVNNHFGPNRNQRLPG---------------YTQYAIGGSMNPSIKSQANLLIAP 207
+MKV V N FGPN QR+P + YAIGGS NP+I S+ N AP
Sbjct: 212 SMKVTVAFNQFGPNAGQRMPRARYGLVHVANNNYDPWNIYAIGGSSNPTILSEGNSFTAP 271
Query: 208 KVGNKKEQTFQVA 220
KKE T ++
Sbjct: 272 SESYKKEVTKRIG 284
Score = 55.1 bits (131), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 26 NVTDQCWRKNPNWHMHQCQVATCSMSFSGKITDNVGKDIVHYKVTDPGDDTINPKLGTLR 85
N D CWR + NW ++ ++A C++ F G D Y VT D+ +NP GTLR
Sbjct: 2 NPIDSCWRGDSNWDQNRMKLADCAVGFGSSTMGGKGGDF--YTVTSTDDNPVNPTPGTLR 59
Query: 86 YGAT 89
YGAT
Sbjct: 60 YGAT 63
>pdb|3VMV|A Chain A, Crystal Structure Of Pectate Lyase Bsp165pela From
Bacillus Sp. N165
pdb|3VMW|A Chain A, Crystal Structure Of Pectate Lyase Bsp165pela From
Bacillus Sp. N165 In Complex With Trigalacturonate
Length = 326
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 40/131 (30%), Positives = 57/131 (43%), Gaps = 26/131 (19%)
Query: 101 AIHPPLLSEGPKPYAIRLVTTSK-VWIDHNIRY---------ECQDGLIDVRRGSTDVTI 150
+IH EG AI + SK VWIDHN Y + DGL+D++R + +T+
Sbjct: 111 SIHHVREGEGT---AIEVTDDSKNVWIDHNEFYSEFPGNGDSDYYDGLVDMKRNAEYITV 167
Query: 151 SNNWFRNQEKRQNM-----------KVIVVNNHFGPNRNQRLPGYTQYAIGGSMNPSIKS 199
S N F N K + K+ +N+F N N R+P +YA N K
Sbjct: 168 SWNKFENHWKTMLVGHTDNASLAPDKITYHHNYFN-NLNSRVP-LIRYADVHMFNNYFKD 225
Query: 200 QANLLIAPKVG 210
+ I +VG
Sbjct: 226 INDTAINSRVG 236
>pdb|2QXZ|A Chain A, Pectate Lyase R236f From Xanthomonas Campestris
pdb|2QXZ|B Chain B, Pectate Lyase R236f From Xanthomonas Campestris
Length = 330
Score = 34.3 bits (77), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 11/50 (22%)
Query: 122 SKVWIDHNIRY----ECQ-------DGLIDVRRGSTDVTISNNWFRNQEK 160
SK+W+DHN + +C DG ID+++G VT+S N+ N +K
Sbjct: 127 SKIWVDHNTVFASLTKCSGAGDASFDGGIDMKKGVHHVTVSYNYVYNYQK 176
>pdb|2QY1|A Chain A, Pectate Lyase A31g/r236f From Xanthomonas Campestris
pdb|2QY1|B Chain B, Pectate Lyase A31g/r236f From Xanthomonas Campestris
Length = 330
Score = 34.3 bits (77), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 11/50 (22%)
Query: 122 SKVWIDHNIRY----ECQ-------DGLIDVRRGSTDVTISNNWFRNQEK 160
SK+W+DHN + +C DG ID+++G VT+S N+ N +K
Sbjct: 127 SKIWVDHNTVFASLTKCSGAGDASFDGGIDMKKGVHHVTVSYNYVYNYQK 176
>pdb|2QX3|A Chain A, Structure Of Pectate Lyase Ii From Xanthomonas Campestris
Pv. Campestris Str. Atcc 33913
pdb|2QX3|B Chain B, Structure Of Pectate Lyase Ii From Xanthomonas Campestris
Pv. Campestris Str. Atcc 33913
Length = 330
Score = 34.3 bits (77), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 11/50 (22%)
Query: 122 SKVWIDHNIRY----ECQ-------DGLIDVRRGSTDVTISNNWFRNQEK 160
SK+W+DHN + +C DG ID+++G VT+S N+ N +K
Sbjct: 127 SKIWVDHNTVFASLTKCSGAGDASFDGGIDMKKGVHHVTVSYNYVYNYQK 176
>pdb|1VBL|A Chain A, Structure Of The Thermostable Pectate Lyase Pl 47
Length = 416
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 25/98 (25%), Positives = 43/98 (43%), Gaps = 31/98 (31%)
Query: 115 AIRLVTTSKVWIDHNIR-----------------YECQDGLIDVRRGSTDVTISNNWFRN 157
+I + +S +WIDHN ++ DG +D++ S +TIS N F N
Sbjct: 191 SISIEGSSHIWIDHNTFTDGDHPDRSLGTYFGRPFQQHDGALDIKNSSDFITISYNVFTN 250
Query: 158 QEK-------------RQNMKVIVVNNHFGPNRNQRLP 182
+K +++V + +N++ N QRLP
Sbjct: 251 HDKVTLIGASDSRMADSGHLRVTLHHNYY-KNVTQRLP 287
>pdb|3ZSC|A Chain A, Catalytic Function And Substrate Recognition Of The
Pectate Lyase From Thermotoga Maritima
Length = 340
Score = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 16/82 (19%)
Query: 116 IRLVTTSKVWIDHNIRYECQDGLIDVRRGSTDVTISNNWFRNQEK--------------- 160
I + + +WIDH DG +D+++ S +T+S N F + +K
Sbjct: 119 INVENSHHIWIDHITFVNGNDGAVDIKKYSNYITVSWNKFVDHDKVSLVGSSDKEDPEQA 178
Query: 161 RQNMKVIVVNNHFGPNRNQRLP 182
Q KV +N+F N QR+P
Sbjct: 179 GQAYKVTYHHNYF-KNLIQRMP 199
>pdb|1OOC|A Chain A, Mutations In The T1.5 Loop Of Pectate Lyase A
pdb|1OOC|B Chain B, Mutations In The T1.5 Loop Of Pectate Lyase A
pdb|1PE9|A Chain A, Mutations In The T1.5 Loop Of Pectate Lyase A
pdb|1PE9|B Chain B, Mutations In The T1.5 Loop Of Pectate Lyase A
Length = 361
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 8/63 (12%)
Query: 98 HLWAIHPPLLSEGPKPYAIRLVTTSKVWIDHNIRYECQDGLIDVRRGSTDVTISNNWFRN 157
H+W H + S+G + + ++ H DG +D++RGS VTISN+
Sbjct: 154 HVWIDHVTI-SDGNFTDDMYTTKDGETYVQH-------DGALDIKRGSDYVTISNSLIDQ 205
Query: 158 QEK 160
+K
Sbjct: 206 HDK 208
>pdb|1JRG|A Chain A, Crystal Structure Of The R3 Form Of Pectate Lyase A,
Erwinia Chrysanthemi
pdb|1JRG|B Chain B, Crystal Structure Of The R3 Form Of Pectate Lyase A,
Erwinia Chrysanthemi
pdb|1JTA|A Chain A, Crystal Structure Of Pectate Lyase A (C2 Form)
Length = 361
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 8/63 (12%)
Query: 98 HLWAIHPPLLSEGPKPYAIRLVTTSKVWIDHNIRYECQDGLIDVRRGSTDVTISNNWFRN 157
H+W H + S+G + + ++ H DG +D++RGS VTISN+
Sbjct: 154 HVWIDHVTI-SDGNFTDDMYTTKDGETYVQH-------DGALDIKRGSDYVTISNSLIDQ 205
Query: 158 QEK 160
+K
Sbjct: 206 HDK 208
>pdb|1E3A|B Chain B, A Slow Processing Precursor Penicillin Acylase From
Escherichia Coli
Length = 560
Score = 28.1 bits (61), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 21/42 (50%), Gaps = 4/42 (9%)
Query: 149 TISNNWFRNQEKRQNMKVIVVNNHFGPNRNQRLPGYTQYAIG 190
T SN W + K Q+ K I+VN GP P YT Y IG
Sbjct: 2 TGSNMWVIGKSKAQDAKAIMVN---GPQFGWYAPAYT-YGIG 39
>pdb|1PCL|A Chain A, Unusual Structural Features In The Parallel Beta-Helix In
Pectate Lyases
Length = 355
Score = 28.1 bits (61), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 17/57 (29%)
Query: 121 TSKVWIDH-----------------NIRYECQDGLIDVRRGSTDVTISNNWFRNQEK 160
++ VW+DH +Y DG +D+++GS VTIS + F +K
Sbjct: 141 STNVWVDHVTISDGSFTDDKYTTKDGEKYVQHDGALDIKKGSDYVTISYSRFELHDK 197
>pdb|1JX9|B Chain B, Penicillin Acylase, Mutant
pdb|1K5Q|B Chain B, Penicillin Acylase, Mutant Complexed With Paa
pdb|1K5S|B Chain B, Penicillin Acylase, Mutant Complexed With Ppa
Length = 557
Score = 28.1 bits (61), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 151 SNNWFRNQEKRQNMKVIVVNNHFGPNRNQRLPGYTQYAIG 190
SN W + K Q+ K I+VN GP P YT Y IG
Sbjct: 1 SNMWVIGKSKAQDAKAIMVN---GPQAGWYAPAYT-YGIG 36
>pdb|1GM8|B Chain B, Crystal Structures Of Penicillin Acylase Enzyme-Substrate
Complexes: Structural Insights Into The Catalytic
Mechanism
pdb|1GM7|B Chain B, Crystal Structures Of Penicillin Acylase Enzyme-Substrate
Complexes: Structural Insights Into The Catalytic
Mechanism
pdb|1GKF|B Chain B, Crystal Structures Of Penicillin Acylase Enzyme-Substrate
Complexes: Structural Insights Into The Catalytic
Mechanism
Length = 557
Score = 27.7 bits (60), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 151 SNNWFRNQEKRQNMKVIVVNNHFGPNRNQRLPGYTQYAIG 190
SN W + K Q+ K I+VN GP P YT Y IG
Sbjct: 1 SNMWVIGKSKAQDAKAIMVN---GPQFGWYAPAYT-YGIG 36
>pdb|1FXH|B Chain B, Mutant Of Penicillin Acylase Impaired In Catalysis With
Phenylacetic Acid In The Active Site
pdb|1FXV|B Chain B, Penicillin Acylase Mutant Impaired In Catalysis With
Penicillin G In The Active Site
Length = 557
Score = 27.7 bits (60), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 151 SNNWFRNQEKRQNMKVIVVNNHFGPNRNQRLPGYTQYAIG 190
SN W + K Q+ K I+VN GP P YT Y IG
Sbjct: 1 SNMWVIGKSKAQDAKAIMVN---GPQFGWYAPAYT-YGIG 36
>pdb|2EWE|A Chain A, Crystal Structure Of Pectate Lyase C R218k Mutant In
Complex With Pentagalacturonic Acid
Length = 353
Score = 27.7 bits (60), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 13/58 (22%)
Query: 116 IRLVTTSKVWIDHN----IRYECQ---------DGLIDVRRGSTDVTISNNWFRNQEK 160
IR+ + VW+DHN +EC + +D++ S VT+S N+ +K
Sbjct: 133 IRVDDSPNVWVDHNELFAANHECDGTPDNDTTFESAVDIKGASNTVTVSYNYIHGVKK 190
>pdb|1PLU|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi With 1 Lu+3 Ion
In The Putative Calcium Binding Site
pdb|1O88|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 11.2 With
30mm Ca2+
pdb|1O8D|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 11.2 With
5mm Ca2+
pdb|1O8E|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 11.2 With
1mm Ca2+
pdb|1O8F|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 9.5 With
30mm Ca2+
pdb|1O8G|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 9.5 With
5mm Ca2+
pdb|1O8H|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 9.5 With
0.3mm Ca2+ Added
pdb|1O8I|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 9.5 With
No Ca2+ Added
pdb|1O8J|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 4.5 With
30mm Ca2+
pdb|1O8K|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 4.5 With
20mm Ca2+
pdb|1O8L|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 4.5 With
5mm Ca2+
pdb|1O8M|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 4.5 With
No Ca2+ Added
pdb|1AIR|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi (Ec16) To A
Resolution Of 2.2 Angstroms With 128 Waters
pdb|2PEC|A Chain A, The Refined Three-Dimensional Structure Of Pectate Lyase C
From Erwinia Chrysanthemi At 2.2 Angstroms Resolution:
Implications For An Enzymatic Mechanism
Length = 353
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 13/58 (22%)
Query: 116 IRLVTTSKVWIDHN----IRYECQ---------DGLIDVRRGSTDVTISNNWFRNQEK 160
IR+ + VW+DHN +EC + +D++ S VT+S N+ +K
Sbjct: 133 IRVDDSPNVWVDHNELFAANHECDGTPDNDTTFESAVDIKGASNTVTVSYNYIHGVKK 190
>pdb|1H2G|B Chain B, Altered Substrate Specificity Mutant Of Penicillin Acylase
Length = 557
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 151 SNNWFRNQEKRQNMKVIVVNNHFGPNRNQRLPGYTQYAIG 190
SN W + K Q+ K I+VN GP P YT Y IG
Sbjct: 1 SNMWVIGKSKAQDAKAIMVN---GPQFGWYAPAYT-YGIG 36
>pdb|1KEC|B Chain B, Penicillin Acylase Mutant With Phenyl Proprionic Acid
Length = 557
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 151 SNNWFRNQEKRQNMKVIVVNNHFGPNRNQRLPGYTQYAIG 190
SN W + K Q+ K I+VN GP P YT Y IG
Sbjct: 1 SNMWVIGKSKAQDAKAIMVN---GPQFGWYAPAYT-YGIG 36
>pdb|1AI4|B Chain B, Penicillin Acylase Complexed With
3,4-Dihydroxyphenylacetic Acid
pdb|1AI5|B Chain B, Penicillin Acylase Complexed With M-Nitrophenylacetic Acid
pdb|1AI6|B Chain B, Penicillin Acylase With P-Hydroxyphenylacetic Acid
pdb|1AI7|B Chain B, Penicillin Acylase Complexed With Phenol
pdb|1AJN|B Chain B, Penicillin Acylase Complexed With P-Nitrophenylacetic Acid
pdb|1AJP|B Chain B, Penicillin Acylase Complexed With
2,5-Dihydroxyphenylacetic Acid
pdb|1AJQ|B Chain B, Penicillin Acylase Complexed With Thiopheneacetic Acid
Length = 557
Score = 27.7 bits (60), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 151 SNNWFRNQEKRQNMKVIVVNNHFGPNRNQRLPGYTQYAIG 190
SN W + K Q+ K I+VN GP P YT Y IG
Sbjct: 1 SNMWVIGKSKAQDAKAIMVN---GPQFGWYAPAYT-YGIG 36
>pdb|1PNK|B Chain B, Penicillin Acylase Has A Single-amino-acid Catalytic
Centre
pdb|1PNL|B Chain B, Penicillin Acylase Has A Single-amino-acid Catalytic
Centre
pdb|1PNM|B Chain B, Penicillin Acylase Has A Single-Amino-Acid Catalytic
Centre
pdb|1GM9|B Chain B, Crystal Structures Of Penicillin Acylase Enzyme-Substrate
Complexes: Structural Insights Into The Catalytic
Mechanism
pdb|1GK9|B Chain B, Crystal Structures Of Penicillin Acylase Enzyme-Substrate
Complexes: Structural Insights Into The Catalytic
Mechanism
pdb|1K7D|B Chain B, Penicillin Acylase With Phenyl Proprionic Acid
Length = 557
Score = 27.7 bits (60), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 151 SNNWFRNQEKRQNMKVIVVNNHFGPNRNQRLPGYTQYAIG 190
SN W + K Q+ K I+VN GP P YT Y IG
Sbjct: 1 SNMWVIGKSKAQDAKAIMVN---GPQFGWYAPAYT-YGIG 36
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 0.132 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,937,916
Number of Sequences: 62578
Number of extensions: 286825
Number of successful extensions: 602
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 582
Number of HSP's gapped (non-prelim): 27
length of query: 234
length of database: 14,973,337
effective HSP length: 96
effective length of query: 138
effective length of database: 8,965,849
effective search space: 1237287162
effective search space used: 1237287162
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)