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= 045655
(377 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 = 115 bits (288), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 60/119 (50%), Positives = 82/119 (68%), Gaps = 3/119 (2%)
Query: 259 VTVAQDGSGNFSTITDAINFAPNNTNVSNGYFLIYITAGVYQEYVSIPKNKINLLMIGDG 318
V VA DGSG++ T+++A+ AP ++ ++I I AGVY+E V +PK K N++ +GDG
Sbjct: 9 VVVAADGSGDYKTVSEAVAAAPEDSKTR---YVIRIKAGVYRENVDVPKKKKNIMFLGDG 65
Query: 319 INQTIITGNRSVVDGWTTFNSATFIVVAPNFVASSITFRNTAGPSKGQAVALRSGADFS 377
TIIT +++V DG TTFNSAT V F+A ITF+NTAG +K QAVALR G+D S
Sbjct: 66 RTSTIITASKNVQDGSTTFNSATVAAVGAGFLARDITFQNTAGAAKHQAVALRVGSDLS 124
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 113 bits (282), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 56/117 (47%), Positives = 79/117 (67%), Gaps = 3/117 (2%)
Query: 261 VAQDGSGNFSTITDAINFAPNNTNVSNGYFLIYITAGVYQEYVSIPKNKINLLMIGDGIN 320
VAQDG+G++ T+ +A+ AP+ + ++IY+ G Y+E V + NK+NL+++GDG+
Sbjct: 7 VAQDGTGDYQTLAEAVAAAPDKSKTR---YVIYVKRGTYKENVEVASNKMNLMIVGDGMY 63
Query: 321 QTIITGNRSVVDGWTTFNSATFIVVAPNFVASSITFRNTAGPSKGQAVALRSGADFS 377
T ITG+ +VVDG TTF SAT V F+ I +NTAGP+K QAVALR GAD S
Sbjct: 64 ATTITGSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMS 120
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/96 (31%), Positives = 50/96 (52%), Gaps = 12/96 (12%)
Query: 269 FSTITDAINFAPNNTNVSNGYFLIYITAGVYQEYVSIPKNKINLLMIGDGINQTIITGNR 328
FS+I A+ AP + F+I++ GVY E + + ++ + L G+ + T+I N
Sbjct: 44 FSSINAALKSAPKDDTP----FIIFLKNGVYTERLEVARSHVTLK--GENRDGTVIGANT 97
Query: 329 SVV------DGWTTFNSATFIVVAPNFVASSITFRN 358
+ + W T S+T +V APNF A ++T RN
Sbjct: 98 AAGMLNPQGEKWGTSGSSTVLVNAPNFTAENLTIRN 133
>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 = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 36/107 (33%), Positives = 52/107 (48%), Gaps = 12/107 (11%)
Query: 258 IVTVAQDGSGNFSTITDAINFAPNNTNVSNGYFLIYITAGVYQEYVSIPKNKINLLMIGD 317
+V+ + F TI DAI AP + F+I I GVY E ++I +N NL + G+
Sbjct: 7 VVSKSSSDGKTFKTIADAIASAPAGSTP----FVILIKNGVYNERLTITRN--NLHLKGE 60
Query: 318 GINQTIITGNRSVV----DG--WTTFNSATFIVVAPNFVASSITFRN 358
N +I + DG W T S+T + A +F A S+T RN
Sbjct: 61 SRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRN 107
>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 = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 36/107 (33%), Positives = 52/107 (48%), Gaps = 12/107 (11%)
Query: 258 IVTVAQDGSGNFSTITDAINFAPNNTNVSNGYFLIYITAGVYQEYVSIPKNKINLLMIGD 317
+V+ + F TI DAI AP + F+I I GVY E ++I +N NL + G+
Sbjct: 7 VVSKSSSDGKTFKTIADAIASAPAGSTP----FVILIKNGVYNERLTITRN--NLHLKGE 60
Query: 318 GINQTIITGNRSVV----DG--WTTFNSATFIVVAPNFVASSITFRN 358
N +I + DG W T S+T + A +F A S+T RN
Sbjct: 61 SRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRN 107
>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 = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 36/107 (33%), Positives = 52/107 (48%), Gaps = 12/107 (11%)
Query: 258 IVTVAQDGSGNFSTITDAINFAPNNTNVSNGYFLIYITAGVYQEYVSIPKNKINLLMIGD 317
+V+ + F TI DAI AP + F+I I GVY E ++I +N NL + G+
Sbjct: 7 VVSKSSSDGKTFKTIADAIASAPAGSTP----FVILIKNGVYNERLTITRN--NLHLKGE 60
Query: 318 GINQTIITGNRSVV----DG--WTTFNSATFIVVAPNFVASSITFRN 358
N +I + DG W T S+T + A +F A S+T RN
Sbjct: 61 SRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRN 107
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 0.374
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,666,637
Number of Sequences: 62578
Number of extensions: 371812
Number of successful extensions: 973
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 960
Number of HSP's gapped (non-prelim): 10
length of query: 377
length of database: 14,973,337
effective HSP length: 100
effective length of query: 277
effective length of database: 8,715,537
effective search space: 2414203749
effective search space used: 2414203749
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: 52 (24.6 bits)