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= 047288
(508 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 = 367 bits (942), Expect = e-102, Method: Compositional matrix adjust.
Identities = 188/322 (58%), Positives = 226/322 (70%), Gaps = 25/322 (7%)
Query: 208 SSGVGPKADVVVAQDGSGNYKTISEGVAAAVKLGGGSKRVVIYVKRGVYRENVEIKRSMK 267
SS VGP +VVVA DGSG+YKT+SE VAAA + R VI +K GVYRENV++ + K
Sbjct: 2 SSTVGP--NVVVAADGSGDYKTVSEAVAAAPE--DSKTRYVIRIKAGVYRENVDVPKKKK 57
Query: 268 NLMLIGDGIDATIVT---------------TVS--GQGFIARDMTFENTAGPANHQAVAL 310
N+M +GDG +TI+T TV+ G GF+ARD+TF+NTAG A HQAVAL
Sbjct: 58 NIMFLGDGRTSTIITASKNVQDGSTTFNSATVAAVGAGFLARDITFQNTAGAAKHQAVAL 117
Query: 311 RSGSDFSVFYSCSFKGYQDTLYVYSQRQFYRNCDIYGTQDFIFGDAAVVLQSCNIYIRKP 370
R GSD S FY C YQD+LYV+S RQF+ NC I GT DFIFG+AAVVLQ C+I+ R+P
Sbjct: 118 RVGSDLSAFYRCDILAYQDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDIHARRP 177
Query: 371 TGGQKNTVTAQGRKDPNENTGIIVHNSRVTAESG----QGSFKSYLGRPWKQYSRTVFMK 426
GQKN VTAQGR DPN+NTGI++ SR+ A S Q SF +YLGRPWK+YSRTV M+
Sbjct: 178 GSGQKNMVTAQGRTDPNQNTGIVIQKSRIGATSDLQPVQSSFPTYLGRPWKEYSRTVVMQ 237
Query: 427 CNIDGVIDPAGWLPWSGSFALSTLYYGEYMNIGTGASTSGRVKWSGYHVIRSPVEAGKFT 486
+I VI+PAGW PW G+FAL TLYYGEY N G GA+TSGRV W G+ VI S EA FT
Sbjct: 238 SSITNVINPAGWFPWDGNFALDTLYYGEYQNTGAGAATSGRVTWKGFKVITSSTEAQGFT 297
Query: 487 VGNFLAGNSWIPATGVPFDSGL 508
G+F+AG SW+ AT PF GL
Sbjct: 298 PGSFIAGGSWLKATTFPFSLGL 319
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 322 bits (824), Expect = 4e-88, Method: Compositional matrix adjust.
Identities = 164/315 (52%), Positives = 202/315 (64%), Gaps = 23/315 (7%)
Query: 215 ADVVVAQDGSGNYKTISEGVAAAVKLGGGSKRVVIYVKRGVYRENVEIKRSMKNLMLIGD 274
A+ VVAQDG+G+Y+T++E VAAA R VIYVKRG Y+ENVE+ + NLM++GD
Sbjct: 3 ANAVVAQDGTGDYQTLAEAVAAAPD--KSKTRYVIYVKRGTYKENVEVASNKMNLMIVGD 60
Query: 275 GIDATIVT-----------------TVSGQGFIARDMTFENTAGPANHQAVALRSGSDFS 317
G+ AT +T GQGFI +D+ +NTAGPA QAVALR G+D S
Sbjct: 61 GMYATTITGSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMS 120
Query: 318 VFYSCSFKGYQDTLYVYSQRQFYRNCDIYGTQDFIFGDAAVVLQSCNIYIRKPTGGQKNT 377
V C YQDTLY +SQRQFYR+ + GT DFIFG+AAVV Q C + RKP Q+N
Sbjct: 121 VINRCRIDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKYQQNM 180
Query: 378 VTAQGRKDPNENTGIIVHNSRVTAESG----QGSFKSYLGRPWKQYSRTVFMKCNIDGVI 433
VTAQGR DPN+ TG + + A S F +YLGRPWK+YSRTV M+ + G+I
Sbjct: 181 VTAQGRTDPNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYLGGLI 240
Query: 434 DPAGWLPWSGSFALSTLYYGEYMNIGTGASTSGRVKWSGYHVIRSPVEAGKFTVGNFLAG 493
+PAGW W G FAL TLYYGE+MN G GA TS RVKW GYHVI P +A FTV + G
Sbjct: 241 NPAGWAEWDGDFALKTLYYGEFMNNGPGAGTSKRVKWPGYHVITDPAKAMPFTVAKLIQG 300
Query: 494 NSWIPATGVPFDSGL 508
SW+ +TGV + GL
Sbjct: 301 GSWLRSTGVAYVDGL 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 = 100 bits (250), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 97/306 (31%), Positives = 134/306 (43%), Gaps = 76/306 (24%)
Query: 227 YKTISEGVAAAVKLGGGSKRVVIYVKRGVYRENVEIKRSMKNLMLIGD------------ 274
+KTI++ +A+A GS VI +K GVY E + I R+ NL L G+
Sbjct: 18 FKTIADAIASAP---AGSTPFVILIKNGVYNERLTITRN--NLHLKGESRNGAVIAAATA 72
Query: 275 -----------GIDATIVTTVSGQGFIARDMTFENTAG-PANH-------------QAVA 309
G + T+S + F A+ +T N PAN QAVA
Sbjct: 73 AGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVA 132
Query: 310 L---RSGSDFSVFYSCSFKGYQDTLYVYSQRQFYRNCDIYGTQDFIFGDAAVVLQSCNIY 366
L +SG D + F S GYQDTLYV R F+ +C I GT DFIFGD + +C++
Sbjct: 133 LYVTKSG-DRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLV 191
Query: 367 IRK----PTGGQKNTVTAQGRKDPNENTGIIVHNSRVTAESGQGSFKSY-LGRPWKQYS- 420
R +G +TA + N+ G+++ NSRV ES KSY LGRPW +
Sbjct: 192 SRYRADVKSGNVSGYLTAPS-TNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTT 250
Query: 421 -------------RTVFMKCNIDGVIDPAGWLPWSGS--------FALSTLYYGEYMNIG 459
+TVF+ ++D I GW SG F + EY + G
Sbjct: 251 FSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYG 308
Query: 460 TGASTS 465
GA+ S
Sbjct: 309 AGAAVS 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 = 100 bits (250), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 97/306 (31%), Positives = 134/306 (43%), Gaps = 76/306 (24%)
Query: 227 YKTISEGVAAAVKLGGGSKRVVIYVKRGVYRENVEIKRSMKNLMLIGD------------ 274
+KTI++ +A+A GS VI +K GVY E + I R+ NL L G+
Sbjct: 18 FKTIADAIASAP---AGSTPFVILIKNGVYNERLTITRN--NLHLKGESRNGAVIAAATA 72
Query: 275 -----------GIDATIVTTVSGQGFIARDMTFENTAG-PANH-------------QAVA 309
G + T+S + F A+ +T N PAN QAVA
Sbjct: 73 AGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVA 132
Query: 310 L---RSGSDFSVFYSCSFKGYQDTLYVYSQRQFYRNCDIYGTQDFIFGDAAVVLQSCNIY 366
L +SG D + F S GYQDTLYV R F+ +C I GT DFIFGD + +C++
Sbjct: 133 LYVTKSG-DRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLV 191
Query: 367 IRK----PTGGQKNTVTAQGRKDPNENTGIIVHNSRVTAESGQGSFKSY-LGRPWKQYS- 420
R +G +TA + N+ G+++ NSRV ES KSY LGRPW +
Sbjct: 192 SRYRADVKSGNVSGYLTAPS-TNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTT 250
Query: 421 -------------RTVFMKCNIDGVIDPAGWLPWSGS--------FALSTLYYGEYMNIG 459
+TVF+ ++D I GW SG F + EY + G
Sbjct: 251 FSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYG 308
Query: 460 TGASTS 465
GA+ S
Sbjct: 309 AGATVS 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 = 97.4 bits (241), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 96/306 (31%), Positives = 133/306 (43%), Gaps = 76/306 (24%)
Query: 227 YKTISEGVAAAVKLGGGSKRVVIYVKRGVYRENVEIKRSMKNLMLIGD------------ 274
+KTI++ +A+A GS VI +K GVY E + I R+ NL L G+
Sbjct: 18 FKTIADAIASAP---AGSTPFVILIKNGVYNERLTITRN--NLHLKGESRNGAVIAAATA 72
Query: 275 -----------GIDATIVTTVSGQGFIARDMTFENTAG-PANH-------------QAVA 309
G + T+S + F A+ +T N PAN QAVA
Sbjct: 73 AGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVA 132
Query: 310 L---RSGSDFSVFYSCSFKGYQDTLYVYSQRQFYRNCDIYGTQDFIFGDAAVVLQSCNIY 366
L +SG D + F S GYQ TLYV R F+ +C I GT DFIFGD + +C++
Sbjct: 133 LYVTKSG-DRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLV 191
Query: 367 IRK----PTGGQKNTVTAQGRKDPNENTGIIVHNSRVTAESGQGSFKSY-LGRPWKQYS- 420
R +G +TA + N+ G+++ NSRV ES KSY LGRPW +
Sbjct: 192 SRYRADVKSGNVSGYLTAPS-TNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTT 250
Query: 421 -------------RTVFMKCNIDGVIDPAGWLPWSGS--------FALSTLYYGEYMNIG 459
+TVF+ ++D I GW SG F + EY + G
Sbjct: 251 FSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYG 308
Query: 460 TGASTS 465
GA+ S
Sbjct: 309 AGATVS 314
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 79.3 bits (194), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 67/217 (30%), Positives = 95/217 (43%), Gaps = 57/217 (26%)
Query: 248 VIYVKRGVYRENVEIKRSMKNLMLIGDGIDATIV-----------------------TTV 284
+I++K GVY E +E+ RS ++ L G+ D T++ V
Sbjct: 62 IIFLKNGVYTERLEVARS--HVTLKGENRDGTVIGANTAAGMLNPQGEKWGTSGSSTVLV 119
Query: 285 SGQGFIARDMTFENTAG-PANH-------------QAVAL--RSGSDFSVFYSCSFKGYQ 328
+ F A ++T N PAN QAVAL SD + F + +GYQ
Sbjct: 120 NAPNFTAENLTIRNDFDFPANKKKADTDPTKLKDTQAVALLLAENSDKARFKAVKLEGYQ 179
Query: 329 DTLYVYS-QRQFYRNCDIYGTQDFIFGDAAVVLQSCNIYIR-----KPTGG---QKNTVT 379
DTLY + R ++ +C+I G DFIFG V +CNI R +P G +T+T
Sbjct: 180 DTLYSKTGSRSYFSDCEISGHVDFIFGSGITVFDNCNIVARDRSDIEPPYGYITAPSTLT 239
Query: 380 AQGRKDPNENTGIIVHNSRVTAESGQGSFKSYLGRPW 416
G+I NSR+T E G + LGRPW
Sbjct: 240 TSPY-------GLIFINSRLTKEPGVPANSFALGRPW 269
>pdb|3GRH|A Chain A, Crystal Structure Of Escherichia Coli Ybhc
Length = 422
Score = 34.7 bits (78), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 40/96 (41%), Gaps = 16/96 (16%)
Query: 288 GFIARDMTFENTAGPA----NHQAVALRSGSDFSVFYSCSFKGYQDTLYVYSQ------- 336
G +++T ENT G + NH AVALR+ D + + G Q+T +V +
Sbjct: 202 GLQLQNLTIENTLGDSVDAGNHPAVALRTDGDQVQINNVNILGRQNTFFVTNSGVQNRLE 261
Query: 337 -----RQFYRNCDIYGTQDFIFGDAAVVLQSCNIYI 367
R N I G D + G AVV + +
Sbjct: 262 TNRQPRTLVTNSYIEGDVDIVSGRGAVVFDNTEFRV 297
>pdb|1X8Z|A Chain A, Crystal Structure Of A Pectin Methylesterase Inhibitor
From Arabidopsis Thaliana
pdb|1X8Z|B Chain B, Crystal Structure Of A Pectin Methylesterase Inhibitor
From Arabidopsis Thaliana
pdb|1X8Z|C Chain C, Crystal Structure Of A Pectin Methylesterase Inhibitor
From Arabidopsis Thaliana
Length = 153
Score = 31.6 bits (70), Expect = 0.96, Method: Composition-based stats.
Identities = 28/115 (24%), Positives = 50/115 (43%), Gaps = 10/115 (8%)
Query: 24 ELITSCSQTPYPEICNHYTATNFLS-NLELGQTQFSFRDLNLKVTIDQAIHAHKLISTMD 82
E+ T C +T P C + T F S NL+ + L T +A K + ++
Sbjct: 7 EMSTICDKTLNPSFCLKFLNTKFASPNLQ------ALAKTTLDSTQARATQTLKKLQSII 60
Query: 83 LSSFNKLAKLALVDCKDLYDDTVNHLNRS---MSSSNPIDSVTWLSAAIANQETC 134
+ +KLA C D Y+ + +L + ++S + + +SAA+ +TC
Sbjct: 61 DGGVDPRSKLAYRSCVDEYESAIGNLEEAFEHLASGDGMGMNMKVSAALDGADTC 115
>pdb|1X91|A Chain A, Crystal Structure Of Mutant Form A Of A Pectin
Methylesterase Inhibitor From Arabidopsis
Length = 153
Score = 31.6 bits (70), Expect = 1.00, Method: Composition-based stats.
Identities = 28/115 (24%), Positives = 50/115 (43%), Gaps = 10/115 (8%)
Query: 24 ELITSCSQTPYPEICNHYTATNFLS-NLELGQTQFSFRDLNLKVTIDQAIHAHKLISTMD 82
E+ T C +T P C + T F S NL+ + L T +A K + ++
Sbjct: 7 EMSTICDKTLNPSFCLKFLNTKFASANLQ------ALAKTTLDSTQARATQTLKKLQSII 60
Query: 83 LSSFNKLAKLALVDCKDLYDDTVNHLNRS---MSSSNPIDSVTWLSAAIANQETC 134
+ +KLA C D Y+ + +L + ++S + + +SAA+ +TC
Sbjct: 61 DGGVDPRSKLAYRSCVDEYESAIGNLEEAFEHLASGDGMGMNMKVSAALDGADTC 115
>pdb|1X90|A Chain A, Crystal Structure Of Mutant Form B Of A Pectin
Methylesterase Inhibitor From Arabidopsis
pdb|1X90|B Chain B, Crystal Structure Of Mutant Form B Of A Pectin
Methylesterase Inhibitor From Arabidopsis
Length = 152
Score = 31.6 bits (70), Expect = 1.0, Method: Composition-based stats.
Identities = 28/115 (24%), Positives = 50/115 (43%), Gaps = 10/115 (8%)
Query: 24 ELITSCSQTPYPEICNHYTATNFLS-NLELGQTQFSFRDLNLKVTIDQAIHAHKLISTMD 82
E+ T C +T P C + T F S NL+ + L T +A K + ++
Sbjct: 6 EMSTICDKTLNPSFCLKFLNTKFASANLQ------ALAKTTLDSTQARATQTLKKLQSII 59
Query: 83 LSSFNKLAKLALVDCKDLYDDTVNHLNRS---MSSSNPIDSVTWLSAAIANQETC 134
+ +KLA C D Y+ + +L + ++S + + +SAA+ +TC
Sbjct: 60 DGGVDPRSKLAYRSCVDEYESAIGNLEEAFEHLASGDGMGMNMKVSAALDGADTC 114
>pdb|1KQF|A Chain A, Formate Dehydrogenase N From E. Coli
pdb|1KQG|A Chain A, Formate Dehydrogenase N From E. Coli
Length = 1015
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 230 ISEGVAAAVKLGGGSKRVVIYVKRGVYRENVEIKRSMKNLMLIGDGIDATIVTTVSGQGF 289
ISE +AAA + G RV + KRG R + R +K L + G ++ + G
Sbjct: 922 ISETLAAAKGINNGD-RVTVSSKRGFIRAVAVVTRRLKPLNVNGQQVETVGIPIHWGFEG 980
Query: 290 IARDMTFENTAGP 302
+AR NT P
Sbjct: 981 VARKGYIANTLTP 993
>pdb|2A1B|A Chain A, Carboxysome Shell Protein Ccmk2
pdb|2A1B|B Chain B, Carboxysome Shell Protein Ccmk2
pdb|2A1B|C Chain C, Carboxysome Shell Protein Ccmk2
pdb|2A1B|D Chain D, Carboxysome Shell Protein Ccmk2
pdb|2A1B|E Chain E, Carboxysome Shell Protein Ccmk2
pdb|2A1B|F Chain F, Carboxysome Shell Protein Ccmk2
pdb|2A1B|G Chain G, Carboxysome Shell Protein Ccmk2
pdb|2A1B|H Chain H, Carboxysome Shell Protein Ccmk2
pdb|2A1B|I Chain I, Carboxysome Shell Protein Ccmk2
pdb|2A1B|J Chain J, Carboxysome Shell Protein Ccmk2
pdb|2A1B|K Chain K, Carboxysome Shell Protein Ccmk2
pdb|2A1B|L Chain L, Carboxysome Shell Protein Ccmk2
Length = 116
Score = 28.9 bits (63), Expect = 7.0, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 8/59 (13%)
Query: 193 GFPTWVSAADR-------RLLQSSGVGP-KADVVVAQDGSGNYKTISEGVAAAVKLGGG 243
GFP V AAD L+ +G + V+V D SG ++S G+ AA ++ GG
Sbjct: 12 GFPAVVEAADSMVKAARVTLVGYEKIGSGRVTVIVRGDVSGVQASVSAGIEAANRVNGG 70
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
0.319 0.134 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,520,186
Number of Sequences: 62578
Number of extensions: 664739
Number of successful extensions: 1433
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1411
Number of HSP's gapped (non-prelim): 23
length of query: 508
length of database: 14,973,337
effective HSP length: 103
effective length of query: 405
effective length of database: 8,527,803
effective search space: 3453760215
effective search space used: 3453760215
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)