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= 044042
(560 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 = 330 bits (847), Expect = 1e-90, Method: Compositional matrix adjust.
Identities = 162/314 (51%), Positives = 209/314 (66%), Gaps = 4/314 (1%)
Query: 246 VTVSQDGKAKFSTINDAITAAPNNTDVTDGYFLIYIKEGVYQEYISIAKNKKILMMXXXX 305
V V+ DG + T+++A+ AAP ++ ++I IK GVY+E + + K KK +M
Sbjct: 9 VVVAADGSGDYKTVSEAVAAAPEDSKTR---YVIRIKAGVYRENVDVPKKKKNIMFLGDG 65
Query: 306 XXXXXXXXXRNFVDGWTTFNSATFAVMAPNFVAVDISFRNTAGPSKHQAVALRSGADLST 365
+N DG TTFNSAT A + F+A DI+F+NTAG +KHQAVALR G+DLS
Sbjct: 66 RTSTIITASKNVQDGSTTFNSATVAAVGAGFLARDITFQNTAGAAKHQAVALRVGSDLSA 125
Query: 366 FYSCSFEGYQDSLYTHSQRQFYRECDIYGTIDFIFGNAAVVLQNCNIYLRLPMSGQYNVI 425
FY C YQDSLY HS RQF+ C I GT+DFIFGNAAVVLQ+C+I+ R P SGQ N++
Sbjct: 126 FYRCDILAYQDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDIHARRPGSGQKNMV 185
Query: 426 TAQGRTDPNQNTGISIHNCTFRAADELALSNQTVQTYLGRPWKEYSRTVIMQSFMDSLIN 485
TAQGRTDPNQNTGI I A +L + TYLGRPWKEYSRTV+MQS + ++IN
Sbjct: 186 TAQGRTDPNQNTGIVIQKSRIGATSDLQPVQSSFPTYLGRPWKEYSRTVVMQSSITNVIN 245
Query: 486 PSGWQIWTGDFALSTLYYAEYDNRGPGSNSANRVTWPGYHVI-NATDAANFTVSNFLLGD 544
P+GW W G+FAL TLYY EY N G G+ ++ RVTW G+ VI ++T+A FT +F+ G
Sbjct: 246 PAGWFPWDGNFALDTLYYGEYQNTGAGAATSGRVTWKGFKVITSSTEAQGFTPGSFIAGG 305
Query: 545 VWLPQTGVPYTGGL 558
WL T P++ GL
Sbjct: 306 SWLKATTFPFSLGL 319
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 327 bits (838), Expect = 1e-89, Method: Compositional matrix adjust.
Identities = 158/312 (50%), Positives = 200/312 (64%), Gaps = 4/312 (1%)
Query: 248 VSQDGKAKFSTINDAITAAPNNTDVTDGYFLIYIKEGVYQEYISIAKNKKILMMXXXXXX 307
V+QDG + T+ +A+ AAP+ + ++IY+K G Y+E + +A NK LM+
Sbjct: 7 VAQDGTGDYQTLAEAVAAAPDKSKTR---YVIYVKRGTYKENVEVASNKMNLMIVGDGMY 63
Query: 308 XXXXXXXRNFVDGWTTFNSATFAVMAPNFVAVDISFRNTAGPSKHQAVALRSGADLSTFY 367
N VDG TTF SAT A + F+ DI +NTAGP+K QAVALR GAD+S
Sbjct: 64 ATTITGSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMSVIN 123
Query: 368 SCSFEGYQDSLYTHSQRQFYRECDIYGTIDFIFGNAAVVLQNCNIYLRLPMSGQYNVITA 427
C + YQD+LY HSQRQFYR+ + GT+DFIFGNAAVV Q C + R P Q N++TA
Sbjct: 124 RCRIDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKYQQNMVTA 183
Query: 428 QGRTDPNQNTGISIHNCTFRAADELALSNQTVQTYLGRPWKEYSRTVIMQSFMDSLINPS 487
QGRTDPNQ TG SI C A+ +L + TYLGRPWKEYSRTV+M+S++ LINP+
Sbjct: 184 QGRTDPNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYLGGLINPA 243
Query: 488 GWQIWTGDFALSTLYYAEYDNRGPGSNSANRVTWPGYHVI-NATDAANFTVSNFLLGDVW 546
GW W GDFAL TLYY E+ N GPG+ ++ RV WPGYHVI + A FTV+ + G W
Sbjct: 244 GWAEWDGDFALKTLYYGEFMNNGPGAGTSKRVKWPGYHVITDPAKAMPFTVAKLIQGGSW 303
Query: 547 LPQTGVPYTGGL 558
L TGV Y GL
Sbjct: 304 LRSTGVAYVDGL 315
>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 = 97.1 bits (240), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 94/302 (31%), Positives = 135/302 (44%), Gaps = 54/302 (17%)
Query: 249 SQDGKAKFSTINDAITAAPNNTDVTDGYFLIYIKEGVYQEYISIAKNKKILMMXXXXXXX 308
S DGK F TI DAI +AP + F+I IK GVY E ++I +N L
Sbjct: 12 SSDGKT-FKTIADAIASAPAGSTP----FVILIKNGVYNERLTITRNNLHLKGESRNGAV 66
Query: 309 XXXXXXRNFV--DG--WTTFNSATFAVMAPNFVAVDISFRNT----AGPSKH-------- 352
+ DG W T S+T + A +F A ++ RN A +K
Sbjct: 67 IAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIK 126
Query: 353 --QAVAL---RSGADLSTFYSCSFEGYQDSLYTHSQRQFYRECDIYGTIDFIFGNAAVVL 407
QAVAL +SG D + F S GYQD+LY R F+ +C I GT+DFIFG+ +
Sbjct: 127 DTQAVALYVTKSG-DRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALF 185
Query: 408 QNCNIYLRLPM---SGQYNVITAQGRTDPNQNTGISIHNC-TFRAADELALSNQTVQTY- 462
NC++ R SG + T+ NQ G+ I N R +D + ++Y
Sbjct: 186 NNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVP-----AKSYG 240
Query: 463 LGRPWKEYS--------------RTVIMQSFMDSLINPSGWQIWTG-DFALSTLYYAEYD 507
LGRPW + +TV + + MD+ I GW +G D +T+++ D
Sbjct: 241 LGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPED 298
Query: 508 NR 509
+R
Sbjct: 299 SR 300
>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 = 96.7 bits (239), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 94/302 (31%), Positives = 135/302 (44%), Gaps = 54/302 (17%)
Query: 249 SQDGKAKFSTINDAITAAPNNTDVTDGYFLIYIKEGVYQEYISIAKNKKILMMXXXXXXX 308
S DGK F TI DAI +AP + F+I IK GVY E ++I +N L
Sbjct: 12 SSDGKT-FKTIADAIASAPAGSTP----FVILIKNGVYNERLTITRNNLHLKGESRNGAV 66
Query: 309 XXXXXXRNFV--DG--WTTFNSATFAVMAPNFVAVDISFRNT----AGPSKH-------- 352
+ DG W T S+T + A +F A ++ RN A +K
Sbjct: 67 IAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIK 126
Query: 353 --QAVAL---RSGADLSTFYSCSFEGYQDSLYTHSQRQFYRECDIYGTIDFIFGNAAVVL 407
QAVAL +SG D + F S GYQD+LY R F+ +C I GT+DFIFG+ +
Sbjct: 127 DTQAVALYVTKSG-DRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALF 185
Query: 408 QNCNIYLRLPM---SGQYNVITAQGRTDPNQNTGISIHNC-TFRAADELALSNQTVQTY- 462
NC++ R SG + T+ NQ G+ I N R +D + ++Y
Sbjct: 186 NNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVP-----AKSYG 240
Query: 463 LGRPWKEYS--------------RTVIMQSFMDSLINPSGWQIWTG-DFALSTLYYAEYD 507
LGRPW + +TV + + MD+ I GW +G D +T+++ D
Sbjct: 241 LGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPED 298
Query: 508 NR 509
+R
Sbjct: 299 SR 300
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 94.4 bits (233), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 88/314 (28%), Positives = 139/314 (44%), Gaps = 57/314 (18%)
Query: 245 IVTVSQDGKAKFSTINDAITAAPNNTDVTDGYFLIYIKEGVYQEYISIAKNKKILMMXXX 304
+V+ + G +FS+IN A+ +AP + D F+I++K GVY E + +A++ L
Sbjct: 34 VVSTTPQGD-EFSSINAALKSAPKD----DTPFIIFLKNGVYTERLEVARSHVTLKGENR 88
Query: 305 XXXXXXXXXXRNFV----DGWTTFNSATFAVMAPNFVAVDISFRNT-----------AGP 349
+ + W T S+T V APNF A +++ RN P
Sbjct: 89 DGTVIGANTAAGMLNPQGEKWGTSGSSTVLVNAPNFTAENLTIRNDFDFPANKKKADTDP 148
Query: 350 SK---HQAVAL--RSGADLSTFYSCSFEGYQDSLYTHS-QRQFYRECDIYGTIDFIFGNA 403
+K QAVAL +D + F + EGYQD+LY+ + R ++ +C+I G +DFIFG+
Sbjct: 149 TKLKDTQAVALLLAENSDKARFKAVKLEGYQDTLYSKTGSRSYFSDCEISGHVDFIFGSG 208
Query: 404 AVVLQNCNIYL--RLPMSGQYNVITAQGRTDPNQNTGISIHNCTFRAADELALSNQTVQT 461
V NCNI R + Y ITA + I I++ R E + +
Sbjct: 209 ITVFDNCNIVARDRSDIEPPYGYITAPSTLTTSPYGLIFINS---RLTKEPGVPANSFA- 264
Query: 462 YLGRPWKEYS--------------RTVIMQSFMDSLINPSGWQIWTG-DFALSTLYYAEY 506
LGRPW + ++V + + MD I GW +G D +++
Sbjct: 265 -LGRPWHPTTTFADGRYADPAAIGQSVFINTTMDDHI--YGWDKMSGKDKQGEKIWFYPQ 321
Query: 507 DNR-------GPGS 513
D+R GPG+
Sbjct: 322 DSRFFEANSQGPGA 335
>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 = 93.6 bits (231), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 93/302 (30%), Positives = 134/302 (44%), Gaps = 54/302 (17%)
Query: 249 SQDGKAKFSTINDAITAAPNNTDVTDGYFLIYIKEGVYQEYISIAKNKKILMMXXXXXXX 308
S DGK F TI DAI +AP + F+I IK GVY E ++I +N L
Sbjct: 12 SSDGKT-FKTIADAIASAPAGSTP----FVILIKNGVYNERLTITRNNLHLKGESRNGAV 66
Query: 309 XXXXXXRNFV--DG--WTTFNSATFAVMAPNFVAVDISFRNT----AGPSKH-------- 352
+ DG W T S+T + A +F A ++ RN A +K
Sbjct: 67 IAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIK 126
Query: 353 --QAVAL---RSGADLSTFYSCSFEGYQDSLYTHSQRQFYRECDIYGTIDFIFGNAAVVL 407
QAVAL +SG D + F S GYQ +LY R F+ +C I GT+DFIFG+ +
Sbjct: 127 DTQAVALYVTKSG-DRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTVDFIFGDGTALF 185
Query: 408 QNCNIYLRLPM---SGQYNVITAQGRTDPNQNTGISIHNC-TFRAADELALSNQTVQTY- 462
NC++ R SG + T+ NQ G+ I N R +D + ++Y
Sbjct: 186 NNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVP-----AKSYG 240
Query: 463 LGRPWKEYS--------------RTVIMQSFMDSLINPSGWQIWTG-DFALSTLYYAEYD 507
LGRPW + +TV + + MD+ I GW +G D +T+++ D
Sbjct: 241 LGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPED 298
Query: 508 NR 509
+R
Sbjct: 299 SR 300
>pdb|3GRH|A Chain A, Crystal Structure Of Escherichia Coli Ybhc
Length = 422
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 38/88 (43%), Gaps = 18/88 (20%)
Query: 340 DISFRNTAGPS----KHQAVALRSGAD------------LSTFYSCSFEGYQDSLYTHSQ 383
+++ NT G S H AVALR+ D +TF+ + G Q+ L T+ Q
Sbjct: 207 NLTIENTLGDSVDAGNHPAVALRTDGDQVQINNVNILGRQNTFF-VTNSGVQNRLETNRQ 265
Query: 384 -RQFYRECDIYGTIDFIFGNAAVVLQNC 410
R I G +D + G AVV N
Sbjct: 266 PRTLVTNSYIEGDVDIVSGRGAVVFDNT 293
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
0.320 0.133 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,010,072
Number of Sequences: 62578
Number of extensions: 572744
Number of successful extensions: 1407
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1385
Number of HSP's gapped (non-prelim): 13
length of query: 560
length of database: 14,973,337
effective HSP length: 104
effective length of query: 456
effective length of database: 8,465,225
effective search space: 3860142600
effective search space used: 3860142600
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: 54 (25.4 bits)