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= 008261
(572 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1GQ8|A Chain A, Pectin Methylesterase From Carrot
Length = 319
Score = 488 bits (1255), Expect = e-138, Method: Compositional matrix adjust.
Identities = 230/305 (75%), Positives = 256/305 (83%)
Query: 268 GSGNYLTXXXXXXXXPEGSSRRYIIRIKAGEYRENVEVPKKKINLMFIGDGRSTTIITGS 327
GSG+Y T PE S RY+IRIKAG YRENV+VPKKK N+MF+GDGR++TIIT S
Sbjct: 15 GSGDYKTVSEAVAAAPEDSKTRYVIRIKAGVYRENVDVPKKKKNIMFLGDGRTSTIITAS 74
Query: 328 RNVVDGSTTFNSATVAVVGDGFLARDITFQNTAGPSKHQAVALRVGSDLSAFYRCDMLAY 387
+NV DGSTTFNSATVA VG GFLARDITFQNTAG +KHQAVALRVGSDLSAFYRCD+LAY
Sbjct: 75 KNVQDGSTTFNSATVAAVGAGFLARDITFQNTAGAAKHQAVALRVGSDLSAFYRCDILAY 134
Query: 388 QDTLYVHSLRQFYTSCIIAGTVDFIFGNAAAVLQNCDIHARRPNPNQRNMVTAQGRDDPN 447
QD+LYVHS RQF+ +C IAGTVDFIFGNAA VLQ+CDIHARRP Q+NMVTAQGR DPN
Sbjct: 135 QDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDIHARRPGSGQKNMVTAQGRTDPN 194
Query: 448 QNTGIVIQKCRIGATSDLLAVKGSFETYLGRPWKRYSRTVVMQSDISDVINPAGWYEWSG 507
QNTGIVIQK RIGATSDL V+ SF TYLGRPWK YSRTVVMQS I++VINPAGW+ W G
Sbjct: 195 QNTGIVIQKSRIGATSDLQPVQSSFPTYLGRPWKEYSRTVVMQSSITNVINPAGWFPWDG 254
Query: 508 NFALDTLFYAEYQNTGAGADTSNRVKWSTFKVITNAAEAQTYTAANFIAGSTWLGSTGFP 567
NFALDTL+Y EYQNTGAGA TS RV W FKVIT++ EAQ +T +FIAG +WL +T FP
Sbjct: 255 NFALDTLYYGEYQNTGAGAATSGRVTWKGFKVITSSTEAQGFTPGSFIAGGSWLKATTFP 314
Query: 568 FSLGL 572
FSLGL
Sbjct: 315 FSLGL 319
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 370 bits (951), Expect = e-103, Method: Compositional matrix adjust.
Identities = 180/305 (59%), Positives = 212/305 (69%)
Query: 268 GSGNYLTXXXXXXXXPEGSSRRYIIRIKAGEYRENVEVPKKKINLMFIGDGRSTTIITGS 327
G+G+Y T P+ S RY+I +K G Y+ENVEV K+NLM +GDG T ITGS
Sbjct: 11 GTGDYQTLAEAVAAAPDKSKTRYVIYVKRGTYKENVEVASNKMNLMIVGDGMYATTITGS 70
Query: 328 RNVVDGSTTFNSATVAVVGDGFLARDITFQNTAGPSKHQAVALRVGSDLSAFYRCDMLAY 387
NVVDGSTTF SAT+A VG GF+ +DI QNTAGP+K QAVALRVG+D+S RC + AY
Sbjct: 71 LNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMSVINRCRIDAY 130
Query: 388 QDTLYVHSLRQFYTSCIIAGTVDFIFGNAAAVLQNCDIHARRPNPNQRNMVTAQGRDDPN 447
QDTLY HS RQFY + GTVDFIFGNAA V Q C + AR+P Q+NMVTAQGR DPN
Sbjct: 131 QDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKYQQNMVTAQGRTDPN 190
Query: 448 QNTGIVIQKCRIGATSDLLAVKGSFETYLGRPWKRYSRTVVMQSDISDVINPAGWYEWSG 507
Q TG IQ C I A+SDL V F TYLGRPWK YSRTVVM+S + +INPAGW EW G
Sbjct: 191 QATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYLGGLINPAGWAEWDG 250
Query: 508 NFALDTLFYAEYQNTGAGADTSNRVKWSTFKVITNAAEAQTYTAANFIAGSTWLGSTGFP 567
+FAL TL+Y E+ N G GA TS RVKW + VIT+ A+A +T A I G +WL STG
Sbjct: 251 DFALKTLYYGEFMNNGPGAGTSKRVKWPGYHVITDPAKAMPFTVAKLIQGGSWLRSTGVA 310
Query: 568 FSLGL 572
+ GL
Sbjct: 311 YVDGL 315
>pdb|2NTB|A Chain A, Crystal Structure Of Pectin Methylesterase In Complex With
Hexasaccharide V
pdb|2NTB|B Chain B, Crystal Structure Of Pectin Methylesterase In Complex With
Hexasaccharide V
pdb|2NTP|A Chain A, Crystal Structure Of Pectin Methylesterase In Complex With
Hexasaccharide Vi
pdb|2NTP|B Chain B, Crystal Structure Of Pectin Methylesterase In Complex With
Hexasaccharide Vi
pdb|2NTQ|A Chain A, Crystal Structure Of Pectin Methylesterase In Complex With
Hexasaccharide Vii
pdb|2NTQ|B Chain B, Crystal Structure Of Pectin Methylesterase In Complex With
Hexasaccharide Vii
Length = 342
Score = 91.7 bits (226), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 93/296 (31%), Positives = 138/296 (46%), Gaps = 59/296 (19%)
Query: 283 PEGSSRRYIIRIKAGEYRENVEVPKKKINLMFIGDGRSTTIITGSRNVV----DGST--T 336
P GS+ ++I IK G Y E + + + NL G+ R+ +I + DGS T
Sbjct: 29 PAGSTP-FVILIKNGVYNERLTITRN--NLHLKGESRNGAVIAAATAAGTLKSDGSKWGT 85
Query: 337 FNSATVAVVGDGFLARDITFQN----TAGPSKH----------QAVALRV--GSDLSAFY 380
S+T+ + F A+ +T +N A +K QAVAL V D + F
Sbjct: 86 AGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVTKSGDRAYFK 145
Query: 381 RCDMLAYQDTLYVHSLRQFYTSCIIAGTVDFIFGNAAAVLQNCDIHARR----PNPNQRN 436
++ YQDTLYV R F++ C I+GTVDFIFG+ A+ NCD+ +R + N
Sbjct: 146 DVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRADVKSGNVSG 205
Query: 437 MVTAQGRDDPNQNTGIVIQKCRIGATSDLLAVKGSFETY-LGRPWK--------RYS--- 484
+TA + NQ G+VI R+ SD + K +Y LGRPW RY+
Sbjct: 206 YLTAPST-NINQKYGLVITNSRVIRESDSVPAK----SYGLGRPWHPTTTFSDGRYADPN 260
Query: 485 ---RTVVMQSDISDVINPAGWYEWSGN--------FALDTLFYAEYQNTGAGADTS 529
+TV + + + + I GW + SG F + + EY++ GAGA S
Sbjct: 261 AIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGATVS 314
>pdb|1QJV|A Chain A, Pectin Methylesterase Pema From Erwinia Chrysanthemi
pdb|1QJV|B Chain B, Pectin Methylesterase Pema From Erwinia Chrysanthemi
Length = 342
Score = 91.3 bits (225), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 93/296 (31%), Positives = 138/296 (46%), Gaps = 59/296 (19%)
Query: 283 PEGSSRRYIIRIKAGEYRENVEVPKKKINLMFIGDGRSTTIITGSRNVV----DGST--T 336
P GS+ ++I IK G Y E + + + NL G+ R+ +I + DGS T
Sbjct: 29 PAGSTP-FVILIKNGVYNERLTITRN--NLHLKGESRNGAVIAAATAAGTLKSDGSKWGT 85
Query: 337 FNSATVAVVGDGFLARDITFQN----TAGPSKH----------QAVALRV--GSDLSAFY 380
S+T+ + F A+ +T +N A +K QAVAL V D + F
Sbjct: 86 AGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVTKSGDRAYFK 145
Query: 381 RCDMLAYQDTLYVHSLRQFYTSCIIAGTVDFIFGNAAAVLQNCDIHARR----PNPNQRN 436
++ YQDTLYV R F++ C I+GTVDFIFG+ A+ NCD+ +R + N
Sbjct: 146 DVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRADVKSGNVSG 205
Query: 437 MVTAQGRDDPNQNTGIVIQKCRIGATSDLLAVKGSFETY-LGRPWK--------RYS--- 484
+TA + NQ G+VI R+ SD + K +Y LGRPW RY+
Sbjct: 206 YLTAPST-NINQKYGLVITNSRVIRESDSVPAK----SYGLGRPWHPTTTFSDGRYADPN 260
Query: 485 ---RTVVMQSDISDVINPAGWYEWSGN--------FALDTLFYAEYQNTGAGADTS 529
+TV + + + + I GW + SG F + + EY++ GAGA S
Sbjct: 261 AIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGAAVS 314
>pdb|2NSP|A Chain A, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide I
pdb|2NSP|B Chain B, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide I
pdb|2NST|A Chain A, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide Ii
pdb|2NST|B Chain B, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide Ii
pdb|2NT6|A Chain A, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide Iii
pdb|2NT6|B Chain B, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide Iii
pdb|2NT9|A Chain A, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide Iv
pdb|2NT9|B Chain B, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide Iv
Length = 342
Score = 88.6 bits (218), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 92/296 (31%), Positives = 137/296 (46%), Gaps = 59/296 (19%)
Query: 283 PEGSSRRYIIRIKAGEYRENVEVPKKKINLMFIGDGRSTTIITGSRNVV----DGST--T 336
P GS+ ++I IK G Y E + + + NL G+ R+ +I + DGS T
Sbjct: 29 PAGSTP-FVILIKNGVYNERLTITRN--NLHLKGESRNGAVIAAATAAGTLKSDGSKWGT 85
Query: 337 FNSATVAVVGDGFLARDITFQN----TAGPSKH----------QAVALRV--GSDLSAFY 380
S+T+ + F A+ +T +N A +K QAVAL V D + F
Sbjct: 86 AGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVTKSGDRAYFK 145
Query: 381 RCDMLAYQDTLYVHSLRQFYTSCIIAGTVDFIFGNAAAVLQNCDIHARR----PNPNQRN 436
++ YQ TLYV R F++ C I+GTVDFIFG+ A+ NCD+ +R + N
Sbjct: 146 DVSLVGYQATLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRADVKSGNVSG 205
Query: 437 MVTAQGRDDPNQNTGIVIQKCRIGATSDLLAVKGSFETY-LGRPWK--------RYS--- 484
+TA + NQ G+VI R+ SD + K +Y LGRPW RY+
Sbjct: 206 YLTAPST-NINQKYGLVITNSRVIRESDSVPAK----SYGLGRPWHPTTTFSDGRYADPN 260
Query: 485 ---RTVVMQSDISDVINPAGWYEWSGN--------FALDTLFYAEYQNTGAGADTS 529
+TV + + + + I GW + SG F + + EY++ GAGA S
Sbjct: 261 AIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGATVS 314
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 68.9 bits (167), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 56/164 (34%), Positives = 78/164 (47%), Gaps = 29/164 (17%)
Query: 290 YIIRIKAGEYRENVEVPKKKINLMFIGDGRSTTIITGSRNVVDGST--------TFNSAT 341
+II +K G Y E +EV + + L G+ R T+I N G T S+T
Sbjct: 61 FIIFLKNGVYTERLEVARSHVTLK--GENRDGTVI--GANTAAGMLNPQGEKWGTSGSST 116
Query: 342 VAVVGDGFLARDITFQNT-----------AGPSK---HQAVALRVG--SDLSAFYRCDML 385
V V F A ++T +N P+K QAVAL + SD + F +
Sbjct: 117 VLVNAPNFTAENLTIRNDFDFPANKKKADTDPTKLKDTQAVALLLAENSDKARFKAVKLE 176
Query: 386 AYQDTLYVHS-LRQFYTSCIIAGTVDFIFGNAAAVLQNCDIHAR 428
YQDTLY + R +++ C I+G VDFIFG+ V NC+I AR
Sbjct: 177 GYQDTLYSKTGSRSYFSDCEISGHVDFIFGSGITVFDNCNIVAR 220
>pdb|3GRH|A Chain A, Crystal Structure Of Escherichia Coli Ybhc
Length = 422
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 39/96 (40%), Gaps = 16/96 (16%)
Query: 347 DGFLARDITFQNTAGPS----KHQAVALRVGSDLSAFYRCDMLAYQDTLYV--------- 393
+G +++T +NT G S H AVALR D ++L Q+T +V
Sbjct: 201 NGLQLQNLTIENTLGDSVDAGNHPAVALRTDGDQVQINNVNILGRQNTFFVTNSGVQNRL 260
Query: 394 ---HSLRQFYTSCIIAGTVDFIFGNAAAVLQNCDIH 426
R T+ I G VD + G A V N +
Sbjct: 261 ETNRQPRTLVTNSYIEGDVDIVSGRGAVVFDNTEFR 296
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
0.318 0.131 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,262,268
Number of Sequences: 62578
Number of extensions: 580960
Number of successful extensions: 1190
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1179
Number of HSP's gapped (non-prelim): 12
length of query: 572
length of database: 14,973,337
effective HSP length: 104
effective length of query: 468
effective length of database: 8,465,225
effective search space: 3961725300
effective search space used: 3961725300
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: 54 (25.4 bits)