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= 043974
(344 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 = 144 bits (364), Expect = 5e-35, Method: Compositional matrix adjust.
Identities = 92/318 (28%), Positives = 148/318 (46%), Gaps = 30/318 (9%)
Query: 36 VAYTISVSRSGGGNFTKIQDAINFIPVNNDQWIRIQISPEIYQEKVTIPQNKPCIFLEGA 95
V + V+ G G++ + +A+ P ++ I+I +Y+E V +P+ K I G
Sbjct: 5 VGPNVVVAADGSGDYKTVSEAVAAAPEDSKTRYVIRIKAGVYRENVDVPKKKKNIMFLGD 64
Query: 96 SSRTTKIQWG----DHDTTISSPTFTSLSENVVAKGILFQNTYNVPPSYRQNQERMEVKQ 151
+T I D TT +S T ++ +A+ I FQNT Q
Sbjct: 65 GRTSTIITASKNVQDGSTTFNSATVAAVGAGFLARDITFQNTAGAAK-----------HQ 113
Query: 152 ALAARISGDKSAFYNCGFAGLQDTLFDDHGRHYFHQCYIEGAIDFIFGNGQSIYHNCAVN 211
A+A R+ D SAFY C QD+L+ R +F C+I G +DFIFGN + +C ++
Sbjct: 114 AVALRVGSDLSAFYRCDILAYQDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDIH 173
Query: 212 VTLKEYLPEKDYGYITAQGRNSTDDPSGFVFTSCQFLGSG---------KAYLGRAYGAF 262
+ +K+ +TAQGR + +G V + + YLGR + +
Sbjct: 174 AR-RPGSGQKN--MVTAQGRTDPNQNTGIVIQKSRIGATSDLQPVQSSFPTYLGRPWKEY 230
Query: 263 SRVIIVNSVLTDMVEPQGWNAWNHVEHEENIEYAEARCRGAGADTSKRVSWEKH---LSV 319
SR +++ S +T+++ P GW W+ + + Y E + GAGA TS RV+W+ S
Sbjct: 231 SRTVVMQSSITNVINPAGWFPWDGNFALDTLYYGEYQNTGAGAATSGRVTWKGFKVITSS 290
Query: 320 DEVKKFTDSSFIDHDGWI 337
E + FT SFI W+
Sbjct: 291 TEAQGFTPGSFIAGGSWL 308
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 124 bits (312), Expect = 6e-29, Method: Compositional matrix adjust.
Identities = 86/313 (27%), Positives = 134/313 (42%), Gaps = 32/313 (10%)
Query: 42 VSRSGGGNFTKIQDAINFIPVNNDQWIRIQISPEIYQEKVTIPQNKPCIFLEG----ASS 97
V++ G G++ + +A+ P + I + Y+E V + NK + + G A++
Sbjct: 7 VAQDGTGDYQTLAEAVAAAPDKSKTRYVIYVKRGTYKENVEVASNKMNLMIVGDGMYATT 66
Query: 98 RTTKIQWGDHDTTISSPTFTSLSENVVAKGILFQNTYNVPPSYRQNQERMEVKQALAARI 157
T + D TT S T ++ + + + I QNT P+ QA+A R+
Sbjct: 67 ITGSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAG--PAK---------DQAVALRV 115
Query: 158 SGDKSAFYNCGFAGLQDTLFDDHGRHYFHQCYIEGAIDFIFGNGQSIYHNCAVNVTLKEY 217
D S C QDTL+ R ++ Y+ G +DFIFGN ++ C L
Sbjct: 116 GADMSVINRCRIDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKC----QLVAR 171
Query: 218 LPEK-DYGYITAQGRNSTDDPSGFVFTSCQFLGSG---------KAYLGRAYGAFSRVII 267
P K +TAQGR + +G C + S YLGR + +SR ++
Sbjct: 172 KPGKYQQNMVTAQGRTDPNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVV 231
Query: 268 VNSVLTDMVEPQGWNAWNHVEHEENIEYAEARCRGAGADTSKRVSWEK-HLSVDEVKK-- 324
+ S L ++ P GW W+ + + Y E G GA TSKRV W H+ D K
Sbjct: 232 MESYLGGLINPAGWAEWDGDFALKTLYYGEFMNNGPGAGTSKRVKWPGYHVITDPAKAMP 291
Query: 325 FTDSSFIDHDGWI 337
FT + I W+
Sbjct: 292 FTVAKLIQGGSWL 304
>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 = 5e-19, Method: Compositional matrix adjust.
Identities = 83/350 (23%), Positives = 155/350 (44%), Gaps = 63/350 (18%)
Query: 40 ISVSRSGGGNFTKIQDAINFIPVNNDQWIRIQISPEIYQEKVTIPQNKPCIFLEGASS-- 97
+S S S G F I DAI P + ++ I I +Y E++TI +N + L+G S
Sbjct: 8 VSKSSSDGKTFKTIADAIASAPAGSTPFV-ILIKNGVYNERLTITRNN--LHLKGESRNG 64
Query: 98 ------------RTTKIQWGDHDTTISSPTFTSLSENVVAKGILFQNTYNVPPSYRQ--- 142
++ +WG T S T T +++ A+ + +N ++ P + +
Sbjct: 65 AVIAAATAAGTLKSDGSKWG----TAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDS 120
Query: 143 NQERMEVKQALAARI--SGDKSAFYNCGFAGLQDTLFDDHGRHYFHQCYIEGAIDFIFGN 200
+ +++ QA+A + SGD++ F + G QDTL+ GR +F C I G +DFIFG+
Sbjct: 121 DSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGD 180
Query: 201 GQSIYHNCAVNVTLKEYLPEKDY-GYITAQGRNSTDDPSGFVFTSCQFLGSGKAYLGRAY 259
G ++++NC + + + + GY+TA N + G V T+ + + + ++Y
Sbjct: 181 GTALFNNCDLVSRYRADVKSGNVSGYLTAPSTN-INQKYGLVITNSRVIRESDSVPAKSY 239
Query: 260 G--------------------AFSRVIIVNSVLTDMVEPQGWNAWNHVE--------HEE 291
G A + + +N+ + + + GW+ + + + E
Sbjct: 240 GLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPE 297
Query: 292 NIEYAEARCRGAGADTSKRVSWEKHLSVDEVKKFTDSSFIDHDGWIAKLP 341
+ + E + GAGA SK + L+ + ++T S + W LP
Sbjct: 298 DSRFFEYKSYGAGATVSKD---RRQLTDAQAAEYTQSKVLGD--WTPTLP 342
>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 = 91.7 bits (226), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 83/350 (23%), Positives = 155/350 (44%), Gaps = 63/350 (18%)
Query: 40 ISVSRSGGGNFTKIQDAINFIPVNNDQWIRIQISPEIYQEKVTIPQNKPCIFLEGASS-- 97
+S S S G F I DAI P + ++ I I +Y E++TI +N + L+G S
Sbjct: 8 VSKSSSDGKTFKTIADAIASAPAGSTPFV-ILIKNGVYNERLTITRNN--LHLKGESRNG 64
Query: 98 ------------RTTKIQWGDHDTTISSPTFTSLSENVVAKGILFQNTYNVPPSYRQ--- 142
++ +WG T S T T +++ A+ + +N ++ P + +
Sbjct: 65 AVIAAATAAGTLKSDGSKWG----TAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDS 120
Query: 143 NQERMEVKQALAARI--SGDKSAFYNCGFAGLQDTLFDDHGRHYFHQCYIEGAIDFIFGN 200
+ +++ QA+A + SGD++ F + G QDTL+ GR +F C I G +DFIFG+
Sbjct: 121 DSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGD 180
Query: 201 GQSIYHNCAVNVTLKEYLPEKDY-GYITAQGRNSTDDPSGFVFTSCQFLGSGKAYLGRAY 259
G ++++NC + + + + GY+TA N + G V T+ + + + ++Y
Sbjct: 181 GTALFNNCDLVSRYRADVKSGNVSGYLTAPSTN-INQKYGLVITNSRVIRESDSVPAKSY 239
Query: 260 G--------------------AFSRVIIVNSVLTDMVEPQGWNAWNHVE--------HEE 291
G A + + +N+ + + + GW+ + + + E
Sbjct: 240 GLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPE 297
Query: 292 NIEYAEARCRGAGADTSKRVSWEKHLSVDEVKKFTDSSFIDHDGWIAKLP 341
+ + E + GAGA SK + L+ + ++T S + W LP
Sbjct: 298 DSRFFEYKSYGAGAAVSKD---RRQLTDAQAAEYTQSKVLGD--WTPTLP 342
>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 = 88.6 bits (218), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 82/350 (23%), Positives = 154/350 (44%), Gaps = 63/350 (18%)
Query: 40 ISVSRSGGGNFTKIQDAINFIPVNNDQWIRIQISPEIYQEKVTIPQNKPCIFLEGASS-- 97
+S S S G F I DAI P + ++ I I +Y E++TI +N + L+G S
Sbjct: 8 VSKSSSDGKTFKTIADAIASAPAGSTPFV-ILIKNGVYNERLTITRNN--LHLKGESRNG 64
Query: 98 ------------RTTKIQWGDHDTTISSPTFTSLSENVVAKGILFQNTYNVPPSYRQ--- 142
++ +WG T S T T +++ A+ + +N ++ P + +
Sbjct: 65 AVIAAATAAGTLKSDGSKWG----TAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDS 120
Query: 143 NQERMEVKQALAARI--SGDKSAFYNCGFAGLQDTLFDDHGRHYFHQCYIEGAIDFIFGN 200
+ +++ QA+A + SGD++ F + G Q TL+ GR +F C I G +DFIFG+
Sbjct: 121 DSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTVDFIFGD 180
Query: 201 GQSIYHNCAVNVTLKEYLPEKDY-GYITAQGRNSTDDPSGFVFTSCQFLGSGKAYLGRAY 259
G ++++NC + + + + GY+TA N + G V T+ + + + ++Y
Sbjct: 181 GTALFNNCDLVSRYRADVKSGNVSGYLTAPSTN-INQKYGLVITNSRVIRESDSVPAKSY 239
Query: 260 G--------------------AFSRVIIVNSVLTDMVEPQGWNAWNHVE--------HEE 291
G A + + +N+ + + + GW+ + + + E
Sbjct: 240 GLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPE 297
Query: 292 NIEYAEARCRGAGADTSKRVSWEKHLSVDEVKKFTDSSFIDHDGWIAKLP 341
+ + E + GAGA SK + L+ + ++T S + W LP
Sbjct: 298 DSRFFEYKSYGAGATVSKD---RRQLTDAQAAEYTQSKVLGD--WTPTLP 342
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 79.0 bits (193), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 77/327 (23%), Positives = 146/327 (44%), Gaps = 61/327 (18%)
Query: 47 GGNFTKIQDAINFIPVNNDQWIRIQISPEIYQEKVTIPQNKPCIFLEGASSRTTKI---- 102
G F+ I A+ P ++ +I I + +Y E++ + ++ + L+G + T I
Sbjct: 41 GDEFSSINAALKSAPKDDTPFI-IFLKNGVYTERLEVARSH--VTLKGENRDGTVIGANT 97
Query: 103 ----------QWGDHDTTISSPTFTSLSENVVAKGILFQNTYNVPPSYRQ---NQERMEV 149
+WG T S T + N A+ + +N ++ P + ++ + +++
Sbjct: 98 AAGMLNPQGEKWG----TSGSSTVLVNAPNFTAENLTIRNDFDFPANKKKADTDPTKLKD 153
Query: 150 KQALAARIS--GDKSAFYNCGFAGLQDTLFDDHG-RHYFHQCYIEGAIDFIFGNGQSIYH 206
QA+A ++ DK+ F G QDTL+ G R YF C I G +DFIFG+G +++
Sbjct: 154 TQAVALLLAENSDKARFKAVKLEGYQDTLYSKTGSRSYFSDCEISGHVDFIFGSGITVFD 213
Query: 207 NCAVNVTLKEYLPEKDYGYITAQGRNSTDDPSGFVFTSCQF-----LGSGKAYLGRAY-- 259
NC + + + E YGYITA +T P G +F + + + + LGR +
Sbjct: 214 NCNIVARDRSDI-EPPYGYITAPSTLTT-SPYGLIFINSRLTKEPGVPANSFALGRPWHP 271
Query: 260 ------------GAFSRVIIVNSVLTDMVEPQGWNAWNHVEHE--------ENIEYAEAR 299
A + + +N+ + D + GW+ + + + ++ + EA
Sbjct: 272 TTTFADGRYADPAAIGQSVFINTTMDDHI--YGWDKMSGKDKQGEKIWFYPQDSRFFEAN 329
Query: 300 CRGAGADTSKRVSWEKHLSVDEVKKFT 326
+G GA ++ + LS +++K FT
Sbjct: 330 SQGPGAAINEG---RRQLSAEQLKAFT 353
>pdb|3GRH|A Chain A, Crystal Structure Of Escherichia Coli Ybhc
Length = 422
Score = 36.6 bits (83), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 32/121 (26%), Positives = 48/121 (39%), Gaps = 18/121 (14%)
Query: 152 ALAARISGDKSAFYNCGFAGLQDTLF------------DDHGRHYFHQCYIEGAIDFIFG 199
A+A R GD+ N G Q+T F + R YIEG +D + G
Sbjct: 225 AVALRTDGDQVQINNVNILGRQNTFFVTNSGVQNRLETNRQPRTLVTNSYIEGDVDIVSG 284
Query: 200 NGQSIYHNCAVNVTLKEYLPEKDYGYITAQGRNSTDDPSGFVFTSCQF--LGSGKAYLGR 257
G ++ N V + ++ Y + A N GF+ + +F G G A LGR
Sbjct: 285 RGAVVFDNTEFRV-VNSRTQQEAYVFAPATLSNIY---YGFLAVNSRFNAFGDGVAQLGR 340
Query: 258 A 258
+
Sbjct: 341 S 341
>pdb|2X8U|A Chain A, Sphingomonas Wittichii Serine Palmitoyltransferase
pdb|2X8U|B Chain B, Sphingomonas Wittichii Serine Palmitoyltransferase
Length = 412
Score = 31.6 bits (70), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 9/75 (12%)
Query: 126 KGILFQNTYNVPPSYRQNQERMEVKQALAARISGDKSAFYNCGFAGLQDTLFDDHGRHYF 185
K ++ + Y++ QE + V + A I D++ + GF F +HGR F
Sbjct: 176 KLVVLEGVYSMMGDIAPLQEMVAVSKKHGAMILVDEA--HGMGF-------FGEHGRGVF 226
Query: 186 HQCYIEGAIDFIFGN 200
+ +E +DF+ G
Sbjct: 227 EEAGVEADVDFVVGT 241
>pdb|2EFJ|A Chain A, The Structure Of 1,7 Dimethylxanthine Methyltransferase
Length = 384
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 12/65 (18%)
Query: 129 LFQNTYN----VPPSYRQNQERMEVKQALAARISGDKSAFYNCGFAGLQDTLFDDHGRHY 184
LFQN +N + PS+ +N E+ ++ + I +FY+ LF + H+
Sbjct: 101 LFQNDFNSVFKLLPSFYRNLEKENGRKIGSCLIGAMPGSFYS--------RLFPEESMHF 152
Query: 185 FHQCY 189
H CY
Sbjct: 153 LHSCY 157
>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 = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 278 PQGWNAWNHVEHEENIEYAEARCRGAGADTSKRVSWEKHLS--VDEVKKFTDSSFIDHD 334
P+G ++V E + Y E R G+D +R+SWE+ S +K D++FI+ +
Sbjct: 93 PKGAGLLDYVNSENRLRYPEYRA--PGSDKWQRISWEEAFSRIAKLMKADRDANFIEKN 149
>pdb|3IKL|A Chain A, Crystal Structure Of Pol Gb Delta-I4.
pdb|3IKL|B Chain B, Crystal Structure Of Pol Gb Delta-I4
Length = 459
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 29/61 (47%)
Query: 271 VLTDMVEPQGWNAWNHVEHEENIEYAEARCRGAGADTSKRVSWEKHLSVDEVKKFTDSSF 330
+LT+ P+G + +H E E N E+ EA G G++ + +H ++ + S
Sbjct: 32 LLTERSSPKGGHVKSHAELEGNGEHPEAPGSGEGSEALLEICQRRHFLSGSKQQLSRDSL 91
Query: 331 I 331
+
Sbjct: 92 L 92
>pdb|2G4C|A Chain A, Crystal Structure Of Human Dna Polymerase Gamma Accessory
Subunit
pdb|2G4C|B Chain B, Crystal Structure Of Human Dna Polymerase Gamma Accessory
Subunit
pdb|2G4C|C Chain C, Crystal Structure Of Human Dna Polymerase Gamma Accessory
Subunit
pdb|2G4C|D Chain D, Crystal Structure Of Human Dna Polymerase Gamma Accessory
Subunit
Length = 474
Score = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 29/61 (47%)
Query: 271 VLTDMVEPQGWNAWNHVEHEENIEYAEARCRGAGADTSKRVSWEKHLSVDEVKKFTDSSF 330
+LT+ P+G + +H E E N E+ EA G G++ + +H ++ + S
Sbjct: 21 LLTERSSPKGGHVKSHAELEGNGEHPEAPGSGEGSEALLEICQRRHFLSGSKQQLSRDSL 80
Query: 331 I 331
+
Sbjct: 81 L 81
>pdb|3T37|A Chain A, Crystal Structure Of Pyridoxine 4-Oxidase From Mesorbium
Loti
Length = 526
Score = 29.3 bits (64), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 24/52 (46%)
Query: 119 LSENVVAKGILFQNTYNVPPSYRQNQERMEVKQALAARISGDKSAFYNCGFA 170
L ++++ G L+ VPPS Q+ E M +A + +G CG A
Sbjct: 305 LQDHLLGAGNLYAARKPVPPSRLQHSESMAYMRADSFTAAGQPEIVVGCGVA 356
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 0.135 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,596,065
Number of Sequences: 62578
Number of extensions: 449812
Number of successful extensions: 800
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 781
Number of HSP's gapped (non-prelim): 13
length of query: 344
length of database: 14,973,337
effective HSP length: 100
effective length of query: 244
effective length of database: 8,715,537
effective search space: 2126591028
effective search space used: 2126591028
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)