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= 008198
(574 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 = 323 bits (828), Expect = 2e-88, Method: Compositional matrix adjust.
Identities = 165/321 (51%), Positives = 211/321 (65%), Gaps = 7/321 (2%)
Query: 249 VNQSVIVSPHGTDNFTTIGDAIAFSPNNSKPEDGYFXXXXXXXXXXXXXXXPKHKKNLLL 308
V +V+V+ G+ ++ T+ +A+A +P +SK + PK KKN++
Sbjct: 5 VGPNVVVAADGSGDYKTVSEAVAAAPEDSKTR---YVIRIKAGVYRENVDVPKKKKNIMF 61
Query: 309 IGDGINRTVITGNHSVIDGWTTFNSSTFAVSGERFVAVDVTFKNTAGPAKHQAVALRNNA 368
+GDG T+IT + +V DG TTFNS+T A G F+A D+TF+NTAG AKHQAVALR +
Sbjct: 62 LGDGRTSTIITASKNVQDGSTTFNSATVAAVGAGFLARDITFQNTAGAAKHQAVALRVGS 121
Query: 369 DLSSFYRCSFEGYQDTLYVHSLRQFYRECDIYGTVDFIFGNAAAVFQNCNIYARKPMPNQ 428
DLS+FYRC YQD+LYVHS RQF+ C I GTVDFIFGNAA V Q+C+I+AR+P Q
Sbjct: 122 DLSAFYRCDILAYQDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDIHARRPGSGQ 181
Query: 429 KNAVTAQGRTDPNQNTGIAIQNCSIVAAPDFAKDLNSTATTLNYLGRPWKEFSRTVYMQS 488
KN VTAQGRTDPNQNTGI IQ I A D +S T YLGRPWKE+SRTV MQS
Sbjct: 182 KNMVTAQGRTDPNQNTGIVIQKSRIGATSDLQPVQSSFPT---YLGRPWKEYSRTVVMQS 238
Query: 489 YIGDLISPVGWLEWNGTVGLDTLYYGEFRNYGPGANTTMRVKWPGYSLMNAS-QALNFTV 547
I ++I+P GW W+G LDTLYYGE++N G GA T+ RV W G+ ++ +S +A FT
Sbjct: 239 SITNVINPAGWFPWDGNFALDTLYYGEYQNTGAGAATSGRVTWKGFKVITSSTEAQGFTP 298
Query: 548 YNFTMGDTWLPDTDIPFCGGL 568
+F G +WL T PF GL
Sbjct: 299 GSFIAGGSWLKATTFPFSLGL 319
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 323 bits (827), Expect = 2e-88, Method: Compositional matrix adjust.
Identities = 159/316 (50%), Positives = 207/316 (65%), Gaps = 7/316 (2%)
Query: 254 IVSPHGTDNFTTIGDAIAFSPNNSKPEDGYFXXXXXXXXXXXXXXXPKHKKNLLLIGDGI 313
+V+ GT ++ T+ +A+A +P+ SK + +K NL+++GDG+
Sbjct: 6 VVAQDGTGDYQTLAEAVAAAPDKSKTR---YVIYVKRGTYKENVEVASNKMNLMIVGDGM 62
Query: 314 NRTVITGNHSVIDGWTTFNSSTFAVSGERFVAVDVTFKNTAGPAKHQAVALRNNADLSSF 373
T ITG+ +V+DG TTF S+T A G+ F+ D+ +NTAGPAK QAVALR AD+S
Sbjct: 63 YATTITGSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMSVI 122
Query: 374 YRCSFEGYQDTLYVHSLRQFYRECDIYGTVDFIFGNAAAVFQNCNIYARKPMPNQKNAVT 433
RC + YQDTLY HS RQFYR+ + GTVDFIFGNAA VFQ C + ARKP Q+N VT
Sbjct: 123 NRCRIDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKYQQNMVT 182
Query: 434 AQGRTDPNQNTGIAIQNCSIVAAPDFAKDLNSTATTLNYLGRPWKEFSRTVYMQSYIGDL 493
AQGRTDPNQ TG +IQ C+I+A+ D L T YLGRPWKE+SRTV M+SY+G L
Sbjct: 183 AQGRTDPNQATGTSIQFCNIIASSDLEPVLKEFPT---YLGRPWKEYSRTVVMESYLGGL 239
Query: 494 ISPVGWLEWNGTVGLDTLYYGEFRNYGPGANTTMRVKWPGYSLM-NASQALNFTVYNFTM 552
I+P GW EW+G L TLYYGEF N GPGA T+ RVKWPGY ++ + ++A+ FTV
Sbjct: 240 INPAGWAEWDGDFALKTLYYGEFMNNGPGAGTSKRVKWPGYHVITDPAKAMPFTVAKLIQ 299
Query: 553 GDTWLPDTDIPFCGGL 568
G +WL T + + GL
Sbjct: 300 GGSWLRSTGVAYVDGL 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 = 88.6 bits (218), Expect = 8e-18, Method: Compositional matrix adjust.
Identities = 101/360 (28%), Positives = 153/360 (42%), Gaps = 80/360 (22%)
Query: 253 VIVSPHGTDN--FTTIGDAIAFSPNNSKP-----EDGYFXXXXXXXXXXXXXXXPKHKKN 305
+VS +D F TI DAIA +P S P ++G + + N
Sbjct: 6 AVVSKSSSDGKTFKTIADAIASAPAGSTPFVILIKNGVYNERLTIT-----------RNN 54
Query: 306 LLLIGDGINRTVITGNHSVI----DG--WTTFNSSTFAVSGERFVAVDVTFKNT----AG 355
L L G+ N VI + DG W T SST +S + F A +T +N A
Sbjct: 55 LHLKGESRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPAN 114
Query: 356 PAKH----------QAVAL--RNNADLSSFYRCSFEGYQDTLYVHSLRQFYRECDIYGTV 403
AK QAVAL + D + F S GYQDTLYV R F+ +C I GTV
Sbjct: 115 QAKSDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTV 174
Query: 404 DFIFGNAAAVFQNCNIYARKPMPNQKNAVTA---QGRTDPNQNTGIAIQNCSIVAAPDFA 460
DFIFG+ A+F NC++ +R + V+ T+ NQ G+ I N ++
Sbjct: 175 DFIFGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVI------ 228
Query: 461 KDLNSTATTLNYLGRPW--------------KEFSRTVYMQSYIGDLISPVGWLEWNGT- 505
++ +S LGRPW +TV++ + + + I GW + +G
Sbjct: 229 RESDSVPAKSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKD 286
Query: 506 VGLDTLYYG-------EFRNYGPGANTTMRVKWPGYSLMNASQALNFTVYNFTMGDTWLP 558
+T+++ E+++YG GA + + + +QA +T +GD W P
Sbjct: 287 KNGNTIWFNPEDSRFFEYKSYGAGATVSKDRR-----QLTDAQAAEYTQSK-VLGD-WTP 339
>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 = 88.6 bits (218), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 94/325 (28%), Positives = 140/325 (43%), Gaps = 73/325 (22%)
Query: 253 VIVSPHGTDN--FTTIGDAIAFSPNNSKP-----EDGYFXXXXXXXXXXXXXXXPKHKKN 305
+VS +D F TI DAIA +P S P ++G + + N
Sbjct: 6 AVVSKSSSDGKTFKTIADAIASAPAGSTPFVILIKNGVYNERLTIT-----------RNN 54
Query: 306 LLLIGDGINRTVITGNHSVI----DG--WTTFNSSTFAVSGERFVAVDVTFKNT----AG 355
L L G+ N VI + DG W T SST +S + F A +T +N A
Sbjct: 55 LHLKGESRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPAN 114
Query: 356 PAKH----------QAVAL--RNNADLSSFYRCSFEGYQDTLYVHSLRQFYRECDIYGTV 403
AK QAVAL + D + F S GYQDTLYV R F+ +C I GTV
Sbjct: 115 QAKSDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTV 174
Query: 404 DFIFGNAAAVFQNCNIYARKPMPNQKNAVTA---QGRTDPNQNTGIAIQNCSIVAAPDFA 460
DFIFG+ A+F NC++ +R + V+ T+ NQ G+ I N ++
Sbjct: 175 DFIFGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVI------ 228
Query: 461 KDLNSTATTLNYLGRPW--------------KEFSRTVYMQSYIGDLISPVGWLEWNGT- 505
++ +S LGRPW +TV++ + + + I GW + +G
Sbjct: 229 RESDSVPAKSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKD 286
Query: 506 VGLDTLYYG-------EFRNYGPGA 523
+T+++ E+++YG GA
Sbjct: 287 KNGNTIWFNPEDSRFFEYKSYGAGA 311
>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 = 85.5 bits (210), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 100/360 (27%), Positives = 152/360 (42%), Gaps = 80/360 (22%)
Query: 253 VIVSPHGTDN--FTTIGDAIAFSPNNSKP-----EDGYFXXXXXXXXXXXXXXXPKHKKN 305
+VS +D F TI DAIA +P S P ++G + + N
Sbjct: 6 AVVSKSSSDGKTFKTIADAIASAPAGSTPFVILIKNGVYNERLTIT-----------RNN 54
Query: 306 LLLIGDGINRTVITGNHSVI----DG--WTTFNSSTFAVSGERFVAVDVTFKNT----AG 355
L L G+ N VI + DG W T SST +S + F A +T +N A
Sbjct: 55 LHLKGESRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPAN 114
Query: 356 PAKH----------QAVAL--RNNADLSSFYRCSFEGYQDTLYVHSLRQFYRECDIYGTV 403
AK QAVAL + D + F S GYQ TLYV R F+ +C I GTV
Sbjct: 115 QAKSDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTV 174
Query: 404 DFIFGNAAAVFQNCNIYARKPMPNQKNAVTA---QGRTDPNQNTGIAIQNCSIVAAPDFA 460
DFIFG+ A+F NC++ +R + V+ T+ NQ G+ I N ++
Sbjct: 175 DFIFGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVI------ 228
Query: 461 KDLNSTATTLNYLGRPW--------------KEFSRTVYMQSYIGDLISPVGWLEWNGT- 505
++ +S LGRPW +TV++ + + + I GW + +G
Sbjct: 229 RESDSVPAKSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKD 286
Query: 506 VGLDTLYYG-------EFRNYGPGANTTMRVKWPGYSLMNASQALNFTVYNFTMGDTWLP 558
+T+++ E+++YG GA + + + +QA +T +GD W P
Sbjct: 287 KNGNTIWFNPEDSRFFEYKSYGAGATVSKDRR-----QLTDAQAAEYTQSK-VLGD-WTP 339
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 76.6 bits (187), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 67/212 (31%), Positives = 95/212 (44%), Gaps = 42/212 (19%)
Query: 239 LGEVESNGILVNQSVIVSPHGTDNFTTIGDAIAFSPNNSKP-----EDGYFXXXXXXXXX 293
LG V N N V +P G D F++I A+ +P + P ++G +
Sbjct: 23 LGTV--NAAQYNAVVSTTPQG-DEFSSINAALKSAPKDDTPFIIFLKNGVYTERLEVA-- 77
Query: 294 XXXXXXPKHKKNLLLIGDGINRTVITGNHSVI------DGWTTFNSSTFAVSGERFVAVD 347
+ ++ L G+ + TVI N + + W T SST V+ F A +
Sbjct: 78 ---------RSHVTLKGENRDGTVIGANTAAGMLNPQGEKWGTSGSSTVLVNAPNFTAEN 128
Query: 348 VTFKNT-----------AGPAK---HQAVAL--RNNADLSSFYRCSFEGYQDTLYVHS-L 390
+T +N P K QAVAL N+D + F EGYQDTLY +
Sbjct: 129 LTIRNDFDFPANKKKADTDPTKLKDTQAVALLLAENSDKARFKAVKLEGYQDTLYSKTGS 188
Query: 391 RQFYRECDIYGTVDFIFGNAAAVFQNCNIYAR 422
R ++ +C+I G VDFIFG+ VF NCNI AR
Sbjct: 189 RSYFSDCEISGHVDFIFGSGITVFDNCNIVAR 220
>pdb|3GRH|A Chain A, Crystal Structure Of Escherichia Coli Ybhc
Length = 422
Score = 33.5 bits (75), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 33/87 (37%), Gaps = 16/87 (18%)
Query: 347 DVTFKNTAG----PAKHQAVALRNNADLSSFYRCSFEGYQDTLYV------------HSL 390
++T +NT G H AVALR + D + G Q+T +V
Sbjct: 207 NLTIENTLGDSVDAGNHPAVALRTDGDQVQINNVNILGRQNTFFVTNSGVQNRLETNRQP 266
Query: 391 RQFYRECDIYGTVDFIFGNAAAVFQNC 417
R I G VD + G A VF N
Sbjct: 267 RTLVTNSYIEGDVDIVSGRGAVVFDNT 293
>pdb|1ZGH|A Chain A, Methionyl-Trna Formyltransferase From Clostridium
Thermocellum
Length = 260
Score = 32.3 bits (72), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 393 FYRECDIYGTVDFIFGNAAAVFQNCNI---YARKPMP-NQKNAVTAQGRTDPNQN 443
F R+ D+YGT + IF A+ + N I ++P+P Q+ T R P Q+
Sbjct: 146 FKRDLDLYGTAEEIFXRASKIIFNDXIPELLTKRPVPQKQEGEATVFQRRKPEQS 200
>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 = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 479 EFSRTVYMQSY--IGDLISPVGWLEWNGTVGLDTLYYGEFRNYGPGANTTMRVKWPGYSL 536
EF++ VY+ IG L GWL G + L YGE+ N +T + PG ++
Sbjct: 270 EFNKNVYVPDVLAIGTLYKQAGWLYGGGLAATNVLDYGEYPNVAYNKSTD---QLPGGAI 326
Query: 537 MNASQALNFTV 547
+N + F V
Sbjct: 327 LNGNWDEVFPV 337
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 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,298,993
Number of Sequences: 62578
Number of extensions: 665754
Number of successful extensions: 1292
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1273
Number of HSP's gapped (non-prelim): 10
length of query: 574
length of database: 14,973,337
effective HSP length: 104
effective length of query: 470
effective length of database: 8,465,225
effective search space: 3978655750
effective search space used: 3978655750
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: 54 (25.4 bits)