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= 039106
(345 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 = 146 bits (369), Expect = 1e-35, Method: Compositional matrix adjust.
Identities = 102/308 (33%), Positives = 147/308 (47%), Gaps = 47/308 (15%)
Query: 74 GNFVTVQKAINSLPVINLCRVVIFISAGTYREKVEIPTTMAYITMIGAGADNTVIEWDDT 133
G++ TV +A+ + P + R VI I AG YRE V++P I +G G +T+I T
Sbjct: 17 GDYKTVSEAVAAAPEDSKTRYVIRIKAGVYRENVDVPKKKKNIMFLGDGRTSTII----T 72
Query: 134 ADRMGQSGRPLGTYASATFAVNSPYFIAKNITFKNKAPLPPSGALGKQAVAFRISADTAA 193
A + Q G T+ SAT A F+A++ITF+N A GA QAVA R+ +D +A
Sbjct: 73 ASKNVQDGST--TFNSATVAAVGAGFLARDITFQNTA-----GAAKHQAVALRVGSDLSA 125
Query: 194 FTGCKFI---------------------GSVDFIFGNGLSFYEDCHLHAITNSYGA---L 229
F C + G+VDFIFGN +DC +HA G +
Sbjct: 126 FYRCDILAYQDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDIHARRPGSGQKNMV 185
Query: 230 TAQKRGSLLEETGFSFVKCKVTGSGAL---------YLGRAWGTFSRVVFAYTYMDKIIT 280
TAQ R + TG K ++ + L YLGR W +SR V + + +I
Sbjct: 186 TAQGRTDPNQNTGIVIQKSRIGATSDLQPVQSSFPTYLGRPWKEYSRTVVMQSSITNVIN 245
Query: 281 PRGWYDWGDKNREMTVFYGQYKCSGPGAYYGGRVSWS--RELTQE-EAEPFISVEFIDGH 337
P GW+ W T++YG+Y+ +G GA GRV+W + +T EA+ F FI G
Sbjct: 246 PAGWFPWDGNFALDTLYYGEYQNTGAGAATSGRVTWKGFKVITSSTEAQGFTPGSFIAGG 305
Query: 338 QWLPSHSL 345
WL + +
Sbjct: 306 SWLKATTF 313
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 120 bits (302), Expect = 8e-28, Method: Compositional matrix adjust.
Identities = 92/305 (30%), Positives = 133/305 (43%), Gaps = 47/305 (15%)
Query: 74 GNFVTVQKAINSLPVINLCRVVIFISAGTYREKVEIPTTMAYITMIGAGADNTVIEWDDT 133
G++ T+ +A+ + P + R VI++ GTY+E VE+ + + ++G G T I T
Sbjct: 13 GDYQTLAEAVAAAPDKSKTRYVIYVKRGTYKENVEVASNKMNLMIVGDGMYATTI----T 68
Query: 134 ADRMGQSGRPLGTYASATFAVNSPYFIAKNITFKNKAPLPPSGALGKQAVAFRISADTAA 193
G T+ SAT A FI ++I +N A G QAVA R+ AD +
Sbjct: 69 GSLNVVDGST--TFRSATLAAVGQGFILQDICIQNTA-----GPAKDQAVALRVGADMSV 121
Query: 194 FTGCKF---------------------IGSVDFIFGNGLSFYEDCHLHAITN---SYGAL 229
C+ G+VDFIFGN ++ C L A +
Sbjct: 122 INRCRIDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKYQQNMV 181
Query: 230 TAQKRGSLLEETGFSFVKCKVTGSGAL---------YLGRAWGTFSRVVFAYTYMDKIIT 280
TAQ R + TG S C + S L YLGR W +SR V +Y+ +I
Sbjct: 182 TAQGRTDPNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYLGGLIN 241
Query: 281 PRGWYDWGDKNREMTVFYGQYKCSGPGAYYGGRVSWS--RELTQ-EEAEPFISVEFIDGH 337
P GW +W T++YG++ +GPGA RV W +T +A PF + I G
Sbjct: 242 PAGWAEWDGDFALKTLYYGEFMNNGPGAGTSKRVKWPGYHVITDPAKAMPFTVAKLIQGG 301
Query: 338 QWLPS 342
WL S
Sbjct: 302 SWLRS 306
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 86.3 bits (212), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 89/330 (26%), Positives = 139/330 (42%), Gaps = 80/330 (24%)
Query: 67 VNKNPRLGNFVTVQKAINSLPVINLCRVVIFISAGTYREKVEIPTTMAYITMIGAGADNT 126
V+ P+ F ++ A+ S P + +IF+ G Y E++E+ +++T+ G D T
Sbjct: 35 VSTTPQGDEFSSINAALKSAPKDD-TPFIIFLKNGVYTERLEV--ARSHVTLKGENRDGT 91
Query: 127 VIEWDDTADRMGQSGRPLGTYASATFAVNSPYFIAKNITFKN---------KAPLPPSGA 177
VI + A + G GT S+T VN+P F A+N+T +N KA P+
Sbjct: 92 VIGANTAAGMLNPQGEKWGTSGSSTVLVNAPNFTAENLTIRNDFDFPANKKKADTDPTKL 151
Query: 178 LGKQAVAFRISADT------------------------AAFTGCKFIGSVDFIFGNGLSF 213
QAVA ++ ++ + F+ C+ G VDFIFG+G++
Sbjct: 152 KDTQAVALLLAENSDKARFKAVKLEGYQDTLYSKTGSRSYFSDCEISGHVDFIFGSGITV 211
Query: 214 YEDCHLHA-----ITNSYGALTAQKRGSLLEET--GFSFVKCKVTG-----SGALYLGRA 261
+++C++ A I YG +TA S L + G F+ ++T + + LGR
Sbjct: 212 FDNCNIVARDRSDIEPPYGYITAP---STLTTSPYGLIFINSRLTKEPGVPANSFALGRP 268
Query: 262 W--------------GTFSRVVFAYTYMDKIITPRGWYDWG--DKNREMTVFYGQ----- 300
W + VF T MD I GW DK E FY Q
Sbjct: 269 WHPTTTFADGRYADPAAIGQSVFINTTMDDHI--YGWDKMSGKDKQGEKIWFYPQDSRFF 326
Query: 301 -YKCSGPGAYYG-GRVSWSRELTQEEAEPF 328
GPGA GR R+L+ E+ + F
Sbjct: 327 EANSQGPGAAINEGR----RQLSAEQLKAF 352
>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 = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 85/335 (25%), Positives = 128/335 (38%), Gaps = 80/335 (23%)
Query: 76 FVTVQKAINSLPVINLCRVVIFISAGTYREKVEIPTTMAYITMIGAGADNTVIEWDDTAD 135
F T+ AI S P VI I G Y E++ I T + + G + VI A
Sbjct: 18 FKTIADAIASAPA-GSTPFVILIKNGVYNERLTI--TRNNLHLKGESRNGAVIAAATAAG 74
Query: 136 RMGQSGRPLGTYASATFAVNSPYFIAKNITFKNKAPLPPSGALGK---------QAVAFR 186
+ G GT S+T +++ F A+++T +N P + A QAVA
Sbjct: 75 TLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALY 134
Query: 187 I--SADTAAF---------------------TGCKFIGSVDFIFGNGLSFYEDCHLHA-- 221
+ S D A F + C+ G+VDFIFG+G + + +C L +
Sbjct: 135 VTKSGDRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRY 194
Query: 222 -----ITNSYGALTA------QKRGSLLEETGFSFVKCKVTGSGALYLGRAW---GTFS- 266
N G LTA QK G ++ + + + + LGR W TFS
Sbjct: 195 RADVKSGNVSGYLTAPSTNINQKYGLVITNSRV-IRESDSVPAKSYGLGRPWHPTTTFSD 253
Query: 267 ----------RVVFAYTYMDKIITPRGWYDWGDKNR---------EMTVFYGQYKCSGPG 307
+ VF T MD I GW K++ E + F+ +YK G G
Sbjct: 254 GRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPEDSRFF-EYKSYGAG 310
Query: 308 AYYGGRVSWSRELTQEEAEPFISVEFIDGHQWLPS 342
A R+LT +A + + + W P+
Sbjct: 311 ATVSKD---RRQLTDAQAAEYTQSKVL--GDWTPT 340
>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 = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 85/335 (25%), Positives = 128/335 (38%), Gaps = 80/335 (23%)
Query: 76 FVTVQKAINSLPVINLCRVVIFISAGTYREKVEIPTTMAYITMIGAGADNTVIEWDDTAD 135
F T+ AI S P VI I G Y E++ I T + + G + VI A
Sbjct: 18 FKTIADAIASAPA-GSTPFVILIKNGVYNERLTI--TRNNLHLKGESRNGAVIAAATAAG 74
Query: 136 RMGQSGRPLGTYASATFAVNSPYFIAKNITFKNKAPLPPSGALGK---------QAVAFR 186
+ G GT S+T +++ F A+++T +N P + A QAVA
Sbjct: 75 TLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALY 134
Query: 187 I--SADTAAF---------------------TGCKFIGSVDFIFGNGLSFYEDCHLHA-- 221
+ S D A F + C+ G+VDFIFG+G + + +C L +
Sbjct: 135 VTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRY 194
Query: 222 -----ITNSYGALTA------QKRGSLLEETGFSFVKCKVTGSGALYLGRAW---GTFS- 266
N G LTA QK G ++ + + + + LGR W TFS
Sbjct: 195 RADVKSGNVSGYLTAPSTNINQKYGLVITNSRV-IRESDSVPAKSYGLGRPWHPTTTFSD 253
Query: 267 ----------RVVFAYTYMDKIITPRGWYDWGDKNR---------EMTVFYGQYKCSGPG 307
+ VF T MD I GW K++ E + F+ +YK G G
Sbjct: 254 GRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPEDSRFF-EYKSYGAG 310
Query: 308 AYYGGRVSWSRELTQEEAEPFISVEFIDGHQWLPS 342
A R+LT +A + + + W P+
Sbjct: 311 ATVSKD---RRQLTDAQAAEYTQSKVL--GDWTPT 340
>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 = 51.2 bits (121), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 85/335 (25%), Positives = 128/335 (38%), Gaps = 80/335 (23%)
Query: 76 FVTVQKAINSLPVINLCRVVIFISAGTYREKVEIPTTMAYITMIGAGADNTVIEWDDTAD 135
F T+ AI S P VI I G Y E++ I T + + G + VI A
Sbjct: 18 FKTIADAIASAPA-GSTPFVILIKNGVYNERLTI--TRNNLHLKGESRNGAVIAAATAAG 74
Query: 136 RMGQSGRPLGTYASATFAVNSPYFIAKNITFKNKAPLPPSGALGK---------QAVAFR 186
+ G GT S+T +++ F A+++T +N P + A QAVA
Sbjct: 75 TLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALY 134
Query: 187 I--SADTAAF---------------------TGCKFIGSVDFIFGNGLSFYEDCHLHA-- 221
+ S D A F + C+ G+VDFIFG+G + + +C L +
Sbjct: 135 VTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRY 194
Query: 222 -----ITNSYGALTA------QKRGSLLEETGFSFVKCKVTGSGALYLGRAW---GTFS- 266
N G LTA QK G ++ + + + + LGR W TFS
Sbjct: 195 RADVKSGNVSGYLTAPSTNINQKYGLVITNSRV-IRESDSVPAKSYGLGRPWHPTTTFSD 253
Query: 267 ----------RVVFAYTYMDKIITPRGWYDWGDKNR---------EMTVFYGQYKCSGPG 307
+ VF T MD I GW K++ E + F+ +YK G G
Sbjct: 254 GRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPEDSRFF-EYKSYGAG 310
Query: 308 AYYGGRVSWSRELTQEEAEPFISVEFIDGHQWLPS 342
A R+LT +A + + + W P+
Sbjct: 311 AAVSKD---RRQLTDAQAAEYTQSKVL--GDWTPT 340
>pdb|2E84|A Chain A, Crystal Structure Of High-Molecular Weight Cytochrome C
From Desulfovibrio Vulgaris (Miyazaki F) In The Presence
Of Zinc Ion
Length = 556
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/84 (22%), Positives = 36/84 (42%), Gaps = 15/84 (17%)
Query: 48 NHSLFQKAKNKFKPCKTIKVN--------KNPRLGNFVTVQKAINSLPVINLCRVVIFIS 99
NH + + A N + C +K++ + + GNFV ++KA++ + C
Sbjct: 305 NHKVHEAASNTCRACHHVKIDNCTTCHTLEGVKDGNFVQIEKAMHQPDSMKSC------- 357
Query: 100 AGTYREKVEIPTTMAYITMIGAGA 123
G + +KV+ P + GA
Sbjct: 358 VGCHNQKVQAPACAGCHGFMKTGA 381
>pdb|2V8I|A Chain A, Structure Of A Family 2 Pectate Lyase In A Native Form
pdb|2V8K|A Chain A, Structure Of A Family 2 Pectate Lyase In Complex With
Trigalacturonic Acid
Length = 543
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 136 RMGQSGRPLGTYASATFAVNSPYFIAKNITFKN 168
R G+ G+P+G + F P+F K ++F N
Sbjct: 168 RHGEYGKPMGALWESKFEQQPPFFATKGLSFLN 200
>pdb|2V8J|A Chain A, Structure Of A Family 2 Pectate Lyase In Complex With A
Transition Metal
Length = 535
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 136 RMGQSGRPLGTYASATFAVNSPYFIAKNITFKN 168
R G+ G+P+G + F P+F K ++F N
Sbjct: 167 RHGEYGKPMGALWESKFEQQPPFFATKGLSFLN 199
>pdb|3IZG|G Chain G, Bacteriophage T7 Prohead Shell Em-Derived Atomic Model
pdb|3IZG|A Chain A, Bacteriophage T7 Prohead Shell Em-Derived Atomic Model
pdb|3IZG|B Chain B, Bacteriophage T7 Prohead Shell Em-Derived Atomic Model
pdb|3IZG|C Chain C, Bacteriophage T7 Prohead Shell Em-Derived Atomic Model
pdb|3IZG|D Chain D, Bacteriophage T7 Prohead Shell Em-Derived Atomic Model
pdb|3IZG|E Chain E, Bacteriophage T7 Prohead Shell Em-Derived Atomic Model
pdb|3IZG|F Chain F, Bacteriophage T7 Prohead Shell Em-Derived Atomic Model
pdb|2XVR|A Chain A, Phage T7 Empty Mature Head Shell
pdb|2XVR|B Chain B, Phage T7 Empty Mature Head Shell
pdb|2XVR|C Chain C, Phage T7 Empty Mature Head Shell
pdb|2XVR|D Chain D, Phage T7 Empty Mature Head Shell
pdb|2XVR|E Chain E, Phage T7 Empty Mature Head Shell
pdb|2XVR|F Chain F, Phage T7 Empty Mature Head Shell
pdb|2XVR|G Chain G, Phage T7 Empty Mature Head Shell
Length = 345
Score = 28.1 bits (61), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 31/108 (28%), Positives = 46/108 (42%), Gaps = 4/108 (3%)
Query: 165 TFKNKAPLPPSGALGKQAVAFRISADTAAFTGCKFIGSVDFIFGNGLSFYEDCHLHAITN 224
T +NKA L ALGK+ +A A AA T ++ + D +F Y + N
Sbjct: 167 TTQNKAALTDQVALGKEIIAALTKA-RAALT-KNYVPAADRVFYCDPDSYSAILAALMPN 224
Query: 225 S--YGALTAQKRGSLLEETGFSFVKCKVTGSGALYLGRAWGTFSRVVF 270
+ Y AL ++GS+ GF V+ +G R T + VF
Sbjct: 225 AANYAALIDPEKGSIRNVMGFEVVEVPHLTAGGAGTAREGTTGQKHVF 272
>pdb|1UD2|A Chain A, Crystal Structure Of Calcium-Free Alpha-Amylase From
Bacillus Sp. Strain Ksm-K38 (Amyk38)
pdb|1UD4|A Chain A, Crystal Structure Of Calcium Free Alpha Amylase From
Bacillus Sp. Strain Ksm-K38 (Amyk38, In Calcium
Containing Solution)
pdb|1UD5|A Chain A, Crystal Structure Of Amyk38 With Rubidium Ion
pdb|1UD6|A Chain A, Crystal Structure Of Amyk38 With Potassium Ion
pdb|1UD8|A Chain A, Crystal Structure Of Amyk38 With Lithium Ion
Length = 480
Score = 28.1 bits (61), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 26/60 (43%), Gaps = 7/60 (11%)
Query: 291 NREMTVF-----YGQYKCSGPGAYYGGRVSWSRELTQEEAEPFISVEFIDGHQWLPSHSL 345
N EM++F Y Y+ S G Y R L EA P +V F+D H P SL
Sbjct: 278 NWEMSLFDVPLNYNFYRASQQGGSYDMRNILRGSLV--EAHPMHAVTFVDNHDTQPGESL 335
>pdb|1UD3|A Chain A, Crystal Structure Of Amyk38 N289h Mutant
Length = 480
Score = 28.1 bits (61), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 26/60 (43%), Gaps = 7/60 (11%)
Query: 291 NREMTVF-----YGQYKCSGPGAYYGGRVSWSRELTQEEAEPFISVEFIDGHQWLPSHSL 345
N EM++F Y Y+ S G Y R L EA P +V F+D H P SL
Sbjct: 278 NWEMSLFDVPLHYNFYRASQQGGSYDMRNILRGSLV--EAHPMHAVTFVDNHDTQPGESL 335
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
0.320 0.135 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,555,559
Number of Sequences: 62578
Number of extensions: 451276
Number of successful extensions: 878
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 859
Number of HSP's gapped (non-prelim): 12
length of query: 345
length of database: 14,973,337
effective HSP length: 100
effective length of query: 245
effective length of database: 8,715,537
effective search space: 2135306565
effective search space used: 2135306565
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: 52 (24.6 bits)