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= 010441
(510 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 = 384 bits (986), Expect = e-107, Method: Compositional matrix adjust.
Identities = 188/312 (60%), Positives = 229/312 (73%), Gaps = 3/312 (0%)
Query: 202 NIVVAQDGSGNVKTIQEXXXXXXXXXXXXXXIYIKAGTYNENIEV--KLKNIMFVGDGIG 259
N+VVA DGSG+ KT+ E I IKAG Y EN++V K KNIMF+GDG
Sbjct: 8 NVVVAADGSGDYKTVSEAVAAAPEDSKTRYVIRIKAGVYRENVDVPKKKKNIMFLGDGRT 67
Query: 260 KTIITGSKSVGGGATTFKSATVAVVGDNFIARDITIRNTAGPNNHQAVALRSGSDLSVFY 319
TIIT SK+V G+TTF SATVA VG F+ARDIT +NTAG HQAVALR GSDLS FY
Sbjct: 68 STIITASKNVQDGSTTFNSATVAAVGAGFLARDITFQNTAGAAKHQAVALRVGSDLSAFY 127
Query: 320 RCSFEGYQDTLYVHSQRQFYRECDIYGTVDFIFGNAAVVLQNCNIFARKP-PNRTNTLTA 378
RC YQD+LYVHS RQF+ C I GTVDFIFGNAAVVLQ+C+I AR+P + N +TA
Sbjct: 128 RCDILAYQDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDIHARRPGSGQKNMVTA 187
Query: 379 QGRTDPNQSTGIIIHNCRVTAASDLKPVQSSVKTFLGRPWKQYSRTVYIKTFLDSLINPA 438
QGRTDPNQ+TGI+I R+ A SDL+PVQSS T+LGRPWK+YSRTV +++ + ++INPA
Sbjct: 188 QGRTDPNQNTGIVIQKSRIGATSDLQPVQSSFPTYLGRPWKEYSRTVVMQSSITNVINPA 247
Query: 439 GWMEWSGDFALNTLYYAEYMNTGPGSSTANRVKWRGYHVLTSPSQVSQFTVGNFIAGNSW 498
GW W G+FAL+TLYY EY NTG G++T+ RV W+G+ V+TS ++ FT G+FIAG SW
Sbjct: 248 GWFPWDGNFALDTLYYGEYQNTGAGAATSGRVTWKGFKVITSSTEAQGFTPGSFIAGGSW 307
Query: 499 LPATNVPFTSGL 510
L AT PF+ GL
Sbjct: 308 LKATTFPFSLGL 319
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 370 bits (950), Expect = e-102, Method: Compositional matrix adjust.
Identities = 179/313 (57%), Positives = 219/313 (69%), Gaps = 3/313 (0%)
Query: 201 ANIVVAQDGSGNVKTIQEXXXXXXXXXXXXXXIYIKAGTYNENIEVKLK--NIMFVGDGI 258
AN VVAQDG+G+ +T+ E IY+K GTY EN+EV N+M VGDG+
Sbjct: 3 ANAVVAQDGTGDYQTLAEAVAAAPDKSKTRYVIYVKRGTYKENVEVASNKMNLMIVGDGM 62
Query: 259 GKTIITGSKSVGGGATTFKSATVAVVGDNFIARDITIRNTAGPNNHQAVALRSGSDLSVF 318
T ITGS +V G+TTF+SAT+A VG FI +DI I+NTAGP QAVALR G+D+SV
Sbjct: 63 YATTITGSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMSVI 122
Query: 319 YRCSFEGYQDTLYVHSQRQFYRECDIYGTVDFIFGNAAVVLQNCNIFARKPPN-RTNTLT 377
RC + YQDTLY HSQRQFYR+ + GTVDFIFGNAAVV Q C + ARKP + N +T
Sbjct: 123 NRCRIDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKYQQNMVT 182
Query: 378 AQGRTDPNQSTGIIIHNCRVTAASDLKPVQSSVKTFLGRPWKQYSRTVYIKTFLDSLINP 437
AQGRTDPNQ+TG I C + A+SDL+PV T+LGRPWK+YSRTV ++++L LINP
Sbjct: 183 AQGRTDPNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYLGGLINP 242
Query: 438 AGWMEWSGDFALNTLYYAEYMNTGPGSSTANRVKWRGYHVLTSPSQVSQFTVGNFIAGNS 497
AGW EW GDFAL TLYY E+MN GPG+ T+ RVKW GYHV+T P++ FTV I G S
Sbjct: 243 AGWAEWDGDFALKTLYYGEFMNNGPGAGTSKRVKWPGYHVITDPAKAMPFTVAKLIQGGS 302
Query: 498 WLPATNVPFTSGL 510
WL +T V + GL
Sbjct: 303 WLRSTGVAYVDGL 315
>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 = 107 bits (267), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 96/285 (33%), Positives = 137/285 (48%), Gaps = 57/285 (20%)
Query: 233 IYIKAGTYNENIEVKLKNIMFVGDGIGKTIITGS------KSVGGGATTFKSATVAVVGD 286
I IK G YNE + + N+ G+ +I + KS G T S+T+ +
Sbjct: 37 ILIKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAK 96
Query: 287 NFIARDITIRNTAG-PNNH-------------QAVAL---RSGSDLSVFYRCSFEGYQDT 329
+F A+ +TIRN P N QAVAL +SG D + F S GYQDT
Sbjct: 97 DFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVTKSG-DRAYFKDVSLVGYQDT 155
Query: 330 LYVHSQRQFYRECDIYGTVDFIFGNAAVVLQNCNIFAR-----KPPNRTNTLTAQGRTDP 384
LYV R F+ +C I GTVDFIFG+ + NC++ +R K N + LTA T+
Sbjct: 156 LYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPS-TNI 214
Query: 385 NQSTGIIIHNCRVTAASDLKPVQSSVKTFLGRPWK--------QYS------RTVYIKTF 430
NQ G++I N RV SD P +S LGRPW +Y+ +TV++ T
Sbjct: 215 NQKYGLVITNSRVIRESDSVPAKSYG---LGRPWHPTTTFSDGRYADPNAIGQTVFLNTS 271
Query: 431 LDSLINPAGWMEWSG-DFALNTLYYA-------EYMNTGPGSSTA 467
+D+ I GW + SG D NT+++ EY + G G++ +
Sbjct: 272 MDNHI--YGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGATVS 314
>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 = 107 bits (267), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 96/285 (33%), Positives = 137/285 (48%), Gaps = 57/285 (20%)
Query: 233 IYIKAGTYNENIEVKLKNIMFVGDGIGKTIITGS------KSVGGGATTFKSATVAVVGD 286
I IK G YNE + + N+ G+ +I + KS G T S+T+ +
Sbjct: 37 ILIKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAK 96
Query: 287 NFIARDITIRNTAG-PNNH-------------QAVAL---RSGSDLSVFYRCSFEGYQDT 329
+F A+ +TIRN P N QAVAL +SG D + F S GYQDT
Sbjct: 97 DFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVTKSG-DRAYFKDVSLVGYQDT 155
Query: 330 LYVHSQRQFYRECDIYGTVDFIFGNAAVVLQNCNIFAR-----KPPNRTNTLTAQGRTDP 384
LYV R F+ +C I GTVDFIFG+ + NC++ +R K N + LTA T+
Sbjct: 156 LYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPS-TNI 214
Query: 385 NQSTGIIIHNCRVTAASDLKPVQSSVKTFLGRPWK--------QYS------RTVYIKTF 430
NQ G++I N RV SD P +S LGRPW +Y+ +TV++ T
Sbjct: 215 NQKYGLVITNSRVIRESDSVPAKS---YGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTS 271
Query: 431 LDSLINPAGWMEWSG-DFALNTLYYA-------EYMNTGPGSSTA 467
+D+ I GW + SG D NT+++ EY + G G++ +
Sbjct: 272 MDNHI--YGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGAAVS 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 = 104 bits (259), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 95/285 (33%), Positives = 136/285 (47%), Gaps = 57/285 (20%)
Query: 233 IYIKAGTYNENIEVKLKNIMFVGDGIGKTIITGS------KSVGGGATTFKSATVAVVGD 286
I IK G YNE + + N+ G+ +I + KS G T S+T+ +
Sbjct: 37 ILIKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAK 96
Query: 287 NFIARDITIRNTAG-PNNH-------------QAVAL---RSGSDLSVFYRCSFEGYQDT 329
+F A+ +TIRN P N QAVAL +SG D + F S GYQ T
Sbjct: 97 DFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVTKSG-DRAYFKDVSLVGYQAT 155
Query: 330 LYVHSQRQFYRECDIYGTVDFIFGNAAVVLQNCNIFAR-----KPPNRTNTLTAQGRTDP 384
LYV R F+ +C I GTVDFIFG+ + NC++ +R K N + LTA T+
Sbjct: 156 LYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPS-TNI 214
Query: 385 NQSTGIIIHNCRVTAASDLKPVQSSVKTFLGRPWK--------QYS------RTVYIKTF 430
NQ G++I N RV SD P +S LGRPW +Y+ +TV++ T
Sbjct: 215 NQKYGLVITNSRVIRESDSVPAKSYG---LGRPWHPTTTFSDGRYADPNAIGQTVFLNTS 271
Query: 431 LDSLINPAGWMEWSG-DFALNTLYYA-------EYMNTGPGSSTA 467
+D+ I GW + SG D NT+++ EY + G G++ +
Sbjct: 272 MDNHI--YGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGATVS 314
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 94.4 bits (233), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 86/256 (33%), Positives = 117/256 (45%), Gaps = 53/256 (20%)
Query: 233 IYIKAGTYNENIEVKLKNIMFVGDGIGKTIITGSKSVGGGAT-------TFKSATVAVVG 285
I++K G Y E +EV ++ G+ T+I G+ + G T S+TV V
Sbjct: 63 IFLKNGVYTERLEVARSHVTLKGENRDGTVI-GANTAAGMLNPQGEKWGTSGSSTVLVNA 121
Query: 286 DNFIARDITIRNTAG-PNNH-------------QAVAL--RSGSDLSVFYRCSFEGYQDT 329
NF A ++TIRN P N QAVAL SD + F EGYQDT
Sbjct: 122 PNFTAENLTIRNDFDFPANKKKADTDPTKLKDTQAVALLLAENSDKARFKAVKLEGYQDT 181
Query: 330 LYVHS-QRQFYRECDIYGTVDFIFGNAAVVLQNCNIFAR-----KPPNRTNTLTAQGRTD 383
LY + R ++ +C+I G VDFIFG+ V NCNI AR +PP T + T
Sbjct: 182 LYSKTGSRSYFSDCEISGHVDFIFGSGITVFDNCNIVARDRSDIEPPYGYITAPSTLTTS 241
Query: 384 PNQSTGIIIHNCRVTAASDLKPVQSSVKTFLGRPWK--------QYS------RTVYIKT 429
P G+I N R+T + P S LGRPW +Y+ ++V+I T
Sbjct: 242 P---YGLIFINSRLTKEPGV-PANSFA---LGRPWHPTTTFADGRYADPAAIGQSVFINT 294
Query: 430 FLDSLINPAGWMEWSG 445
+D I GW + SG
Sbjct: 295 TMDDHI--YGWDKMSG 308
>pdb|3GRH|A Chain A, Crystal Structure Of Escherichia Coli Ybhc
Length = 422
Score = 35.4 bits (80), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 36/87 (41%), Gaps = 16/87 (18%)
Query: 291 RDITIRNTAGPN----NHQAVALRSGSDLSVFYRCSFEGYQDTLYV------------HS 334
+++TI NT G + NH AVALR+ D + G Q+T +V
Sbjct: 206 QNLTIENTLGDSVDAGNHPAVALRTDGDQVQINNVNILGRQNTFFVTNSGVQNRLETNRQ 265
Query: 335 QRQFYRECDIYGTVDFIFGNAAVVLQN 361
R I G VD + G AVV N
Sbjct: 266 PRTLVTNSYIEGDVDIVSGRGAVVFDN 292
>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 = 35.0 bits (79), Expect = 0.11, Method: Composition-based stats.
Identities = 39/159 (24%), Positives = 63/159 (39%), Gaps = 12/159 (7%)
Query: 22 GYSPEEVKSWCGKTPNPQPCEYFLTQKTDVTSIKQDTDFYKISLQLALERATTAQSRTYT 81
G E+ + C KT NP C FL K +++ K +L RAT + +
Sbjct: 1 GAMSSEMSTICDKTLNPSFCLKFLNTKFASANLQA---LAKTTLDSTQARATQTLKKLQS 57
Query: 82 LGSKCRNEREKAAWEDCRELYELTVLKLNQTSNSSPGCTKVDKQTWLSSALTNLETCRAS 141
+ + R K A+ C + YE + L + + +S+AL +TC
Sbjct: 58 IIDGGVDPRSKLAYRSCVDEYESAIGNLEEAFEHLASGDGMGMNMKVSAALDGADTC--- 114
Query: 142 LEDLGVPEYVLPLLSNNVTKLISNTLSL-----NKVPYN 175
L+D+ V + NN +K I N + N +P N
Sbjct: 115 LDDVKRLRSVDSSVVNN-SKTIKNLCGIALVISNMLPRN 152
>pdb|1X91|A Chain A, Crystal Structure Of Mutant Form A Of A Pectin
Methylesterase Inhibitor From Arabidopsis
Length = 153
Score = 34.3 bits (77), Expect = 0.15, Method: Composition-based stats.
Identities = 38/154 (24%), Positives = 62/154 (40%), Gaps = 12/154 (7%)
Query: 27 EVKSWCGKTPNPQPCEYFLTQKTDVTSIKQDTDFYKISLQLALERATTAQSRTYTLGSKC 86
E+ + C KT NP C FL K +++ K +L RAT + ++
Sbjct: 7 EMSTICDKTLNPSFCLKFLNTKFASANLQA---LAKTTLDSTQARATQTLKKLQSIIDGG 63
Query: 87 RNEREKAAWEDCRELYELTVLKLNQTSNSSPGCTKVDKQTWLSSALTNLETCRASLEDLG 146
+ R K A+ C + YE + L + + +S+AL +TC L+D+
Sbjct: 64 VDPRSKLAYRSCVDEYESAIGNLEEAFEHLASGDGMGMNMKVSAALDGADTC---LDDVK 120
Query: 147 VPEYVLPLLSNNVTKLISNTLSL-----NKVPYN 175
V + NN +K I N + N +P N
Sbjct: 121 RLRSVDSSVVNN-SKTIKNLCGIALVISNMLPRN 153
>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 = 33.9 bits (76), Expect = 0.21, Method: Composition-based stats.
Identities = 38/154 (24%), Positives = 62/154 (40%), Gaps = 12/154 (7%)
Query: 27 EVKSWCGKTPNPQPCEYFLTQKTDVTSIKQDTDFYKISLQLALERATTAQSRTYTLGSKC 86
E+ + C KT NP C FL K +++ K +L RAT + ++
Sbjct: 7 EMSTICDKTLNPSFCLKFLNTKFASPNLQA---LAKTTLDSTQARATQTLKKLQSIIDGG 63
Query: 87 RNEREKAAWEDCRELYELTVLKLNQTSNSSPGCTKVDKQTWLSSALTNLETCRASLEDLG 146
+ R K A+ C + YE + L + + +S+AL +TC L+D+
Sbjct: 64 VDPRSKLAYRSCVDEYESAIGNLEEAFEHLASGDGMGMNMKVSAALDGADTC---LDDVK 120
Query: 147 VPEYVLPLLSNNVTKLISNTLSL-----NKVPYN 175
V + NN +K I N + N +P N
Sbjct: 121 RLRSVDSSVVNN-SKTIKNLCGIALVISNMLPRN 153
>pdb|3RGW|L Chain L, Crystal Structure At 1.5 A Resolution Of An H2-Reduced,
O2-Tolerant Hydrogenase From Ralstonia Eutropha Unmasks
A Novel Iron-Sulfur Cluster
Length = 603
Score = 28.9 bits (63), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 420 QYSRTVYIKTFL--DSLINPAGWMEWSGDFALNTLYYAEYMNTGPGSST 466
++++ VY+ L +L AGW+ G A N L Y EY N ST
Sbjct: 270 EFNKNVYVPDVLAIGTLYKQAGWLYGGGLAATNVLDYGEYPNVAYNKST 318
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 0.132 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,784,676
Number of Sequences: 62578
Number of extensions: 592695
Number of successful extensions: 1431
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1409
Number of HSP's gapped (non-prelim): 23
length of query: 510
length of database: 14,973,337
effective HSP length: 103
effective length of query: 407
effective length of database: 8,527,803
effective search space: 3470815821
effective search space used: 3470815821
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)