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= 039887
(241 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 = 125 bits (313), Expect = 3e-29, Method: Compositional matrix adjust.
Identities = 70/163 (42%), Positives = 93/163 (57%), Gaps = 10/163 (6%)
Query: 72 ITVCQNGTGDFKTIREAINSIPPYNTRRVILEIKPGVYREKVSIPKPLPFVTFLGNSSDP 131
+ V +G+GD+KT+ EA+ + P + R ++ IK GVYRE V +PK + FLG+
Sbjct: 9 VVVAADGSGDYKTVSEAVAAAPEDSKTRYVIRIKAGVYRENVDVPKKKKNIMFLGDGRTS 68
Query: 132 PTITGNDTASATGSDGKPLKTFQSATVAVDANYFVAINMKFENTAPHVVGSMGEQAVALR 191
IT AS DG TF SATVA F+A ++ F+NTA G+ QAVALR
Sbjct: 69 TIIT----ASKNVQDGS--TTFNSATVAAVGAGFLARDITFQNTA----GAAKHQAVALR 118
Query: 192 ISGTKAAFYNCSFYGAQDTLYDHKGLHYFNNCFIQGSVDFIFG 234
+ +AFY C QD+LY H +F NCFI G+VDFIFG
Sbjct: 119 VGSDLSAFYRCDILAYQDSLYVHSNRQFFINCFIAGTVDFIFG 161
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 92.8 bits (229), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 55/168 (32%), Positives = 88/168 (52%), Gaps = 10/168 (5%)
Query: 74 VCQNGTGDFKTIREAINSIPPYNTRRVILEIKPGVYREKVSIPKPLPFVTFLGNSSDPPT 133
V Q+GTGD++T+ EA+ + P + R ++ +K G Y+E V + + +G+ T
Sbjct: 7 VAQDGTGDYQTLAEAVAAAPDKSKTRYVIYVKRGTYKENVEVASNKMNLMIVGDGMYATT 66
Query: 134 ITGNDTASATGSDGKPLKTFQSATVAVDANYFVAINMKFENTAPHVVGSMGEQAVALRIS 193
ITG S DG TF+SAT+A F+ ++ +NTA G +QAVALR+
Sbjct: 67 ITG----SLNVVDGS--TTFRSATLAAVGQGFILQDICIQNTA----GPAKDQAVALRVG 116
Query: 194 GTKAAFYNCSFYGAQDTLYDHKGLHYFNNCFIQGSVDFIFGYGRSLYE 241
+ C QDTLY H ++ + ++ G+VDFIFG +++
Sbjct: 117 ADMSVINRCRIDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQ 164
>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 = 77.0 bits (188), Expect = 9e-15, Method: Compositional matrix adjust.
Identities = 62/171 (36%), Positives = 84/171 (49%), Gaps = 15/171 (8%)
Query: 82 FKTIREAINSIPPYNTRRVILEIKPGVYREKVSIPKPLPFVTFLGNSSDPPTITGNDTAS 141
FKTI +AI S P +T VIL IK GVY E+++I + + G S + I A
Sbjct: 18 FKTIADAIASAPAGSTPFVIL-IKNGVYNERLTITRNN--LHLKGESRNGAVIAAATAAG 74
Query: 142 ATGSDGKPLKTFQSATVAVDANYFVAINMKFENTAPHVVGSMGE----------QAVALR 191
SDG T S+T+ + A F A ++ N QAVAL
Sbjct: 75 TLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALY 134
Query: 192 I--SGTKAAFYNCSFYGAQDTLYDHKGLHYFNNCFIQGSVDFIFGYGRSLY 240
+ SG +A F + S G QDTLY G +F++C I G+VDFIFG G +L+
Sbjct: 135 VTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALF 185
>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 = 76.6 bits (187), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 62/171 (36%), Positives = 84/171 (49%), Gaps = 15/171 (8%)
Query: 82 FKTIREAINSIPPYNTRRVILEIKPGVYREKVSIPKPLPFVTFLGNSSDPPTITGNDTAS 141
FKTI +AI S P +T VIL IK GVY E+++I + + G S + I A
Sbjct: 18 FKTIADAIASAPAGSTPFVIL-IKNGVYNERLTITRNN--LHLKGESRNGAVIAAATAAG 74
Query: 142 ATGSDGKPLKTFQSATVAVDANYFVAINMKFENTAPHVVGSMGE----------QAVALR 191
SDG T S+T+ + A F A ++ N QAVAL
Sbjct: 75 TLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALY 134
Query: 192 I--SGTKAAFYNCSFYGAQDTLYDHKGLHYFNNCFIQGSVDFIFGYGRSLY 240
+ SG +A F + S G QDTLY G +F++C I G+VDFIFG G +L+
Sbjct: 135 VTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALF 185
>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 = 73.6 bits (179), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 61/171 (35%), Positives = 83/171 (48%), Gaps = 15/171 (8%)
Query: 82 FKTIREAINSIPPYNTRRVILEIKPGVYREKVSIPKPLPFVTFLGNSSDPPTITGNDTAS 141
FKTI +AI S P +T VIL IK GVY E+++I + + G S + I A
Sbjct: 18 FKTIADAIASAPAGSTPFVIL-IKNGVYNERLTITRNN--LHLKGESRNGAVIAAATAAG 74
Query: 142 ATGSDGKPLKTFQSATVAVDANYFVAINMKFENTAPHVVGSMGE----------QAVALR 191
SDG T S+T+ + A F A ++ N QAVAL
Sbjct: 75 TLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALY 134
Query: 192 I--SGTKAAFYNCSFYGAQDTLYDHKGLHYFNNCFIQGSVDFIFGYGRSLY 240
+ SG +A F + S G Q TLY G +F++C I G+VDFIFG G +L+
Sbjct: 135 VTKSGDRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTVDFIFGDGTALF 185
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 72.8 bits (177), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 61/190 (32%), Positives = 86/190 (45%), Gaps = 18/190 (9%)
Query: 65 AETNKVRITVCQNGTGDFKTIREAINSIPPYNTRRVILEIKPGVYREKVSIPKPLPFVTF 124
A+ N V T Q +F +I A+ S P +T +I +K GVY E++ + + VT
Sbjct: 29 AQYNAVVSTTPQGD--EFSSINAALKSAPKDDTPFIIF-LKNGVYTERLEVARS--HVTL 83
Query: 125 LGNSSDPPTITGNDTASATGSDGKPLKTFQSATVAVDANYFVAINMKFEN---------- 174
G + D I N A G+ T S+TV V+A F A N+ N
Sbjct: 84 KGENRDGTVIGANTAAGMLNPQGEKWGTSGSSTVLVNAPNFTAENLTIRNDFDFPANKKK 143
Query: 175 --TAPHVVGSMGEQAVALRISGTKAAFYNCSFYGAQDTLYDHKGLH-YFNNCFIQGSVDF 231
T P + A+ L + KA F G QDTLY G YF++C I G VDF
Sbjct: 144 ADTDPTKLKDTQAVALLLAENSDKARFKAVKLEGYQDTLYSKTGSRSYFSDCEISGHVDF 203
Query: 232 IFGYGRSLYE 241
IFG G ++++
Sbjct: 204 IFGSGITVFD 213
>pdb|3GRH|A Chain A, Crystal Structure Of Escherichia Coli Ybhc
Length = 422
Score = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 12/85 (14%)
Query: 169 NMKFENTAPHVVGSMGEQAVALRISGTKAAFYNCSFYGAQDTLY------------DHKG 216
N+ ENT V + AVALR G + N + G Q+T + + +
Sbjct: 207 NLTIENTLGDSVDAGNHPAVALRTDGDQVQINNVNILGRQNTFFVTNSGVQNRLETNRQP 266
Query: 217 LHYFNNCFIQGSVDFIFGYGRSLYE 241
N +I+G VD + G G +++
Sbjct: 267 RTLVTNSYIEGDVDIVSGRGAVVFD 291
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 0.134 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,081,525
Number of Sequences: 62578
Number of extensions: 283455
Number of successful extensions: 678
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 663
Number of HSP's gapped (non-prelim): 7
length of query: 241
length of database: 14,973,337
effective HSP length: 96
effective length of query: 145
effective length of database: 8,965,849
effective search space: 1300048105
effective search space used: 1300048105
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)