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= 009545
(532 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 312 bits (800), Expect = 2e-85, Method: Compositional matrix adjust.
Identities = 169/317 (53%), Positives = 208/317 (65%), Gaps = 13/317 (4%)
Query: 227 INANVIVAQDGTGNYRTVSEAISAA---SGNRFVIYVKAGVYKEKIR--TNKDGITLIGD 281
I AN +VAQDGTG+Y+T++EA++AA S R+VIYVK G YKE + +NK + ++GD
Sbjct: 1 IIANAVVAQDGTGDYQTLAEAVAAAPDKSKTRYVIYVKRGTYKENVEVASNKMNLMIVGD 60
Query: 282 GKYTTIITGDDNARRGTSMPATATFS---DGFIARDIGFHNTAGPQGEQALALNVASDHT 338
G Y T ITG N G++ +AT + GFI +DI NTAGP +QA+AL V +D +
Sbjct: 61 GMYATTITGSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMS 120
Query: 339 VFYRCSIAGYQDTLYALALRQFYRDTDIYGTIDFIFGNAAAVFQNCYLVLRRPKGSY--N 396
V RC I YQDTLYA + RQFYRD+ + GT+DFIFGNAA VFQ C LV R+P G Y N
Sbjct: 121 VINRCRIDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKP-GKYQQN 179
Query: 397 AITANGRTDPGQNTGFSLQNCKIAAGSDYAPVKHKYNSYLGRPWKQYSRAVVMQXXXXXX 456
+TA GRTDP Q TG S+Q C I A SD PV ++ +YLGRPWK+YSR VVM+
Sbjct: 180 MVTAQGRTDPNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYLGGL 239
Query: 457 XXXXGWVEWPGAGGYANTLYFAEYANVGPGAATSNRVKWPGFHVI-GPDVAVKFTVANFI 515
GW EW G TLY+ E+ N GPGA TS RVKWPG+HVI P A+ FTVA I
Sbjct: 240 INPAGWAEWDGDFAL-KTLYYGEFMNNGPGAGTSKRVKWPGYHVITDPAKAMPFTVAKLI 298
Query: 516 AGTSWLPSTGVIFDGGL 532
G SWL STGV + GL
Sbjct: 299 QGGSWLRSTGVAYVDGL 315
>pdb|1GQ8|A Chain A, Pectin Methylesterase From Carrot
Length = 319
Score = 286 bits (731), Expect = 2e-77, Method: Compositional matrix adjust.
Identities = 157/317 (49%), Positives = 199/317 (62%), Gaps = 13/317 (4%)
Query: 227 INANVIVAQDGTGNYRTVSEAISAA---SGNRFVIYVKAGVYKEKIRT--NKDGITLIGD 281
+ NV+VA DG+G+Y+TVSEA++AA S R+VI +KAGVY+E + K I +GD
Sbjct: 5 VGPNVVVAADGSGDYKTVSEAVAAAPEDSKTRYVIRIKAGVYRENVDVPKKKKNIMFLGD 64
Query: 282 GKYTTIITGDDNARRGTSMPATATFSD---GFIARDIGFHNTAGPQGEQALALNVASDHT 338
G+ +TIIT N + G++ +AT + GF+ARDI F NTAG QA+AL V SD +
Sbjct: 65 GRTSTIITASKNVQDGSTTFNSATVAAVGAGFLARDITFQNTAGAAKHQAVALRVGSDLS 124
Query: 339 VFYRCSIAGYQDTLYALALRQFYRDTDIYGTIDFIFGNAAAVFQNCYLVLRRP-KGSYNA 397
FYRC I YQD+LY + RQF+ + I GT+DFIFGNAA V Q+C + RRP G N
Sbjct: 125 AFYRCDILAYQDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDIHARRPGSGQKNM 184
Query: 398 ITANGRTDPGQNTGFSLQNCKIAAGSDYAPVKHKYNSYLGRPWKQYSRAVVMQXXXXXXX 457
+TA GRTDP QNTG +Q +I A SD PV+ + +YLGRPWK+YSR VVMQ
Sbjct: 185 VTAQGRTDPNQNTGIVIQKSRIGATSDLQPVQSSFPTYLGRPWKEYSRTVVMQSSITNVI 244
Query: 458 XXXGWVEWPGAGGYA-NTLYFAEYANVGPGAATSNRVKWPGFHVIGPDVAVK-FTVANFI 515
GW W G +A +TLY+ EY N G GAATS RV W GF VI + FT +FI
Sbjct: 245 NPAGWFPWD--GNFALDTLYYGEYQNTGAGAATSGRVTWKGFKVITSSTEAQGFTPGSFI 302
Query: 516 AGTSWLPSTGVIFDGGL 532
AG SWL +T F GL
Sbjct: 303 AGGSWLKATTFPFSLGL 319
>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 = 93.2 bits (230), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 91/318 (28%), Positives = 137/318 (43%), Gaps = 55/318 (17%)
Query: 224 APRINANVIVAQDGTGNYRTVSEAISAASGNR--FVIYVKAGVYKEKIRTNKDGITLIGD 281
A NA V + ++T+++AI++A FVI +K GVY E++ ++ + L G+
Sbjct: 1 ATTYNAVVSKSSSDGKTFKTIADAIASAPAGSTPFVILIKNGVYNERLTITRNNLHLKGE 60
Query: 282 GKYTTIITG--------DDNARRGTSMPATATFS-DGFIARDIGFHN------------- 319
+ +I D ++ GT+ +T T S F A+ + N
Sbjct: 61 SRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDS 120
Query: 320 -TAGPQGEQALALNV--ASDHTVFYRCSIAGYQDTLYALALRQFYRDTDIYGTIDFIFGN 376
++ + QA+AL V + D F S+ GYQDTLY R F+ D I GT+DFIFG+
Sbjct: 121 DSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGD 180
Query: 377 AAAVFQNCYLVLRR----PKGSYNAITANGRTDPGQNTGFSLQNCKIAAGSDYAPVKHKY 432
A+F NC LV R G+ + T+ Q G + N ++ SD P K
Sbjct: 181 GTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVPAK--- 237
Query: 433 NSY-LGRPWK--------QYSRAVVMQXX----XXXXXXXXGWVEWPGAGGYANTLYFA- 478
SY LGRPW +Y+ + GW + G NT++F
Sbjct: 238 -SYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHIYGWDKMSGKDKNGNTIWFNP 296
Query: 479 ------EYANVGPGAATS 490
EY + G GAA S
Sbjct: 297 EDSRFFEYKSYGAGAAVS 314
>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 = 77/249 (30%), Positives = 116/249 (46%), Gaps = 36/249 (14%)
Query: 224 APRINANVIVAQDGTGNYRTVSEAISAASGNR--FVIYVKAGVYKEKIRTNKDGITLIGD 281
A NA V + ++T+++AI++A FVI +K GVY E++ ++ + L G+
Sbjct: 1 ATTYNAVVSKSSSDGKTFKTIADAIASAPAGSTPFVILIKNGVYNERLTITRNNLHLKGE 60
Query: 282 GKYTTIITG--------DDNARRGTSMPATATFS-DGFIARDIGFHN------------- 319
+ +I D ++ GT+ +T T S F A+ + N
Sbjct: 61 SRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDS 120
Query: 320 -TAGPQGEQALALNV--ASDHTVFYRCSIAGYQDTLYALALRQFYRDTDIYGTIDFIFGN 376
++ + QA+AL V + D F S+ GYQDTLY R F+ D I GT+DFIFG+
Sbjct: 121 DSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGD 180
Query: 377 AAAVFQNCYLVLRR----PKGSYNAITANGRTDPGQNTGFSLQNCKIAAGSDYAPVKHKY 432
A+F NC LV R G+ + T+ Q G + N ++ SD P K
Sbjct: 181 GTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVPAK--- 237
Query: 433 NSY-LGRPW 440
SY LGRPW
Sbjct: 238 -SYGLGRPW 245
>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 = 88.2 bits (217), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 76/249 (30%), Positives = 115/249 (46%), Gaps = 36/249 (14%)
Query: 224 APRINANVIVAQDGTGNYRTVSEAISAASGNR--FVIYVKAGVYKEKIRTNKDGITLIGD 281
A NA V + ++T+++AI++A FVI +K GVY E++ ++ + L G+
Sbjct: 1 ATTYNAVVSKSSSDGKTFKTIADAIASAPAGSTPFVILIKNGVYNERLTITRNNLHLKGE 60
Query: 282 GKYTTIITG--------DDNARRGTSMPATATFS-DGFIARDIGFHN------------- 319
+ +I D ++ GT+ +T T S F A+ + N
Sbjct: 61 SRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDS 120
Query: 320 -TAGPQGEQALALNV--ASDHTVFYRCSIAGYQDTLYALALRQFYRDTDIYGTIDFIFGN 376
++ + QA+AL V + D F S+ GYQ TLY R F+ D I GT+DFIFG+
Sbjct: 121 DSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTVDFIFGD 180
Query: 377 AAAVFQNCYLVLRR----PKGSYNAITANGRTDPGQNTGFSLQNCKIAAGSDYAPVKHKY 432
A+F NC LV R G+ + T+ Q G + N ++ SD P K
Sbjct: 181 GTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVPAK--- 237
Query: 433 NSY-LGRPW 440
SY LGRPW
Sbjct: 238 -SYGLGRPW 245
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 71.2 bits (173), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 56/189 (29%), Positives = 93/189 (49%), Gaps = 29/189 (15%)
Query: 230 NVIVAQDGTGN-YRTVSEAISAASGNR--FVIYVKAGVYKEKIRTNKDGITLIGDGKYTT 286
N +V+ G+ + +++ A+ +A + F+I++K GVY E++ + +TL G+ + T
Sbjct: 32 NAVVSTTPQGDEFSSINAALKSAPKDDTPFIIFLKNGVYTERLEVARSHVTLKGENRDGT 91
Query: 287 IITGDDNA--------RRGTSMPATATF-SDGFIARDIGFHNT-----------AGP--- 323
+I + A + GTS +T + F A ++ N P
Sbjct: 92 VIGANTAAGMLNPQGEKWGTSGSSTVLVNAPNFTAENLTIRNDFDFPANKKKADTDPTKL 151
Query: 324 QGEQALALNVA--SDHTVFYRCSIAGYQDTLYA-LALRQFYRDTDIYGTIDFIFGNAAAV 380
+ QA+AL +A SD F + GYQDTLY+ R ++ D +I G +DFIFG+ V
Sbjct: 152 KDTQAVALLLAENSDKARFKAVKLEGYQDTLYSKTGSRSYFSDCEISGHVDFIFGSGITV 211
Query: 381 FQNCYLVLR 389
F NC +V R
Sbjct: 212 FDNCNIVAR 220
>pdb|3FRW|A Chain A, Crystal Structure Of Putative Trpr Protein From
Ruminococcus Obeum
pdb|3FRW|B Chain B, Crystal Structure Of Putative Trpr Protein From
Ruminococcus Obeum
pdb|3FRW|C Chain C, Crystal Structure Of Putative Trpr Protein From
Ruminococcus Obeum
pdb|3FRW|D Chain D, Crystal Structure Of Putative Trpr Protein From
Ruminococcus Obeum
pdb|3FRW|E Chain E, Crystal Structure Of Putative Trpr Protein From
Ruminococcus Obeum
pdb|3FRW|F Chain F, Crystal Structure Of Putative Trpr Protein From
Ruminococcus Obeum
pdb|3FRW|G Chain G, Crystal Structure Of Putative Trpr Protein From
Ruminococcus Obeum
pdb|3FRW|H Chain H, Crystal Structure Of Putative Trpr Protein From
Ruminococcus Obeum
Length = 107
Score = 30.4 bits (67), Expect = 2.4, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 11/74 (14%)
Query: 129 KNKDDIQTWLGAALTFQQTCKDSVNSL-GLSERNEVIKKISQKMDYL--SQLTSNPLALV 185
KNK++ T+ F+ C ++N L LS+R EV K ++ K YL S+ T A +
Sbjct: 24 KNKEECYTF------FEDVC--TINELLSLSQRFEVAKXLTDKRTYLDISEKTGASTATI 75
Query: 186 NRIARASYPKNSTY 199
+R+ R+ N Y
Sbjct: 76 SRVNRSLNYGNDGY 89
>pdb|1NCJ|A Chain A, N-Cadherin, Two-Domain Fragment
Length = 215
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 41/92 (44%), Gaps = 23/92 (25%)
Query: 227 INANVIVAQDGTGNYRTVSEAISAASGNRF--------VIYVKAGVYKEKIRTNKDGITL 278
I+A+ A +G YR VS+A S S N F +I V AG+ +EK++
Sbjct: 133 IDADDPNALNGMLRYRIVSQAPSTPSPNMFTINNETGDIITVAAGLDREKVQ-------- 184
Query: 279 IGDGKYTTIITGDD---NARRGTSMPATATFS 307
+YT II D N G S ATA +
Sbjct: 185 ----QYTLIIQATDMEGNPTYGLSNTATAVIT 212
>pdb|2J9Y|B Chain B, Tryptophan Synthase Q114n Mutant In Complex With Compound
Ii
Length = 397
Score = 29.6 bits (65), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 39/95 (41%), Gaps = 1/95 (1%)
Query: 168 SQKMDYLSQLTSNPLALVNRIARASYPKNSTYNRRLDEEQGDFPNWVSAKNRKLLQAPRI 227
+Q D L P AL + + + Y +R D G + LL A R+
Sbjct: 43 AQFADLLKNYAGRPTALTKCQNITAGTRTTLYLKREDLLHGGAHKTNQVLGQALL-AKRM 101
Query: 228 NANVIVAQDGTGNYRTVSEAISAASGNRFVIYVKA 262
+ I+A+ G GN+ S SA G + IY+ A
Sbjct: 102 GKSEIIAETGAGNHGVASALASALLGLKCRIYMGA 136
>pdb|3Q2W|A Chain A, Crystal Structure Of Mouse N-Cadherin Ectodomain
Length = 559
Score = 29.6 bits (65), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 29/92 (31%), Positives = 41/92 (44%), Gaps = 23/92 (25%)
Query: 227 INANVIVAQDGTGNYRTVSEAISAASGNRF--------VIYVKAGVYKEKIRTNKDGITL 278
I+A+ A +G YR +S+A S S N F +I V AG+ +EK++
Sbjct: 133 IDADDPNALNGMLRYRILSQAPSTPSPNMFTINNETGDIITVAAGLDREKVQ-------- 184
Query: 279 IGDGKYTTIITGDD---NARRGTSMPATATFS 307
+YT II D N G S ATA +
Sbjct: 185 ----QYTLIIQATDMEGNPTYGLSNTATAVIT 212
>pdb|2QVI|A Chain A, Crystal Structure Of N-Cadherin Domains Ec12
Length = 215
Score = 29.3 bits (64), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 29/92 (31%), Positives = 41/92 (44%), Gaps = 23/92 (25%)
Query: 227 INANVIVAQDGTGNYRTVSEAISAASGNRF--------VIYVKAGVYKEKIRTNKDGITL 278
I+A+ A +G YR +S+A S S N F +I V AG+ +EK++
Sbjct: 133 IDADDPNALNGMLRYRILSQAPSTPSPNMFTINNETGDIITVAAGLDREKVQ-------- 184
Query: 279 IGDGKYTTIITGDD---NARRGTSMPATATFS 307
+YT II D N G S ATA +
Sbjct: 185 ----QYTLIIQATDMEGNPTYGLSNTATAVIT 212
>pdb|2J9Z|B Chain B, Tryptophan Synthase T110 Mutant Complex
Length = 397
Score = 29.3 bits (64), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 39/95 (41%), Gaps = 1/95 (1%)
Query: 168 SQKMDYLSQLTSNPLALVNRIARASYPKNSTYNRRLDEEQGDFPNWVSAKNRKLLQAPRI 227
+Q D L P AL + + + Y +R D G + LL A R+
Sbjct: 43 AQFADLLKNYAGRPTALTKCQNITAGTRTTLYLKREDLLHGGAHKTNQVLGQALL-AKRM 101
Query: 228 NANVIVAQDGTGNYRTVSEAISAASGNRFVIYVKA 262
+ I+A+ G GN+ S SA G + IY+ A
Sbjct: 102 GKSEIIAEVGAGNHGVASALASALLGLKCRIYMGA 136
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 0.133 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,838,877
Number of Sequences: 62578
Number of extensions: 642265
Number of successful extensions: 1364
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1340
Number of HSP's gapped (non-prelim): 16
length of query: 532
length of database: 14,973,337
effective HSP length: 103
effective length of query: 429
effective length of database: 8,527,803
effective search space: 3658427487
effective search space used: 3658427487
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)