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= 043374
(567 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 = 354 bits (909), Expect = 6e-98, Method: Compositional matrix adjust.
Identities = 173/314 (55%), Positives = 220/314 (70%), Gaps = 4/314 (1%)
Query: 253 VTVALDGTGNFSTITDAINVAPNNTNPDNGYFLIYVTAGVYQEYISIPKNKKNLMMIGDG 312
V VA DG+G++ T+++A+ AP ++ ++I + AGVY+E + +PK KKN+M +GDG
Sbjct: 9 VVVAADGSGDYKTVSEAVAAAPEDSKTR---YVIRIKAGVYRENVDVPKKKKNIMFLGDG 65
Query: 313 INQTIITGNRNVVDGWTTSNSATFIVVAPNFVASDITIRNTAGAVKHQAVALRSAADLST 372
TIIT ++NV DG TT NSAT V F+A DIT +NTAGA KHQAVALR +DLS
Sbjct: 66 RTSTIITASKNVQDGSTTFNSATVAAVGAGFLARDITFQNTAGAAKHQAVALRVGSDLSA 125
Query: 373 FYSCSFEGYQDTLYTHSLRQFYRECDIYGTVDFIFGNAAVVLQNCNIYPRLPMSGQFNAI 432
FY C YQD+LY HS RQF+ C I GTVDFIFGNAAVVLQ+C+I+ R P SGQ N +
Sbjct: 126 FYRCDILAYQDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDIHARRPGSGQKNMV 185
Query: 433 TAQGRTDPNQNTGTSIHNCTIRASNDLASGSQTVQTYLGRPWKEYSRTVYMQTFMDSLIN 492
TAQGRTDPNQNTG I I A++DL + TYLGRPWKEYSRTV MQ+ + ++IN
Sbjct: 186 TAQGRTDPNQNTGIVIQKSRIGATSDLQPVQSSFPTYLGRPWKEYSRTVVMQSSITNVIN 245
Query: 493 PAGWHDWSGDFALSTLYYAEYNNTGPGSDTTNRVTWPGYHII-DATEAANFTVSNFLSGD 551
PAGW W G+FAL TLYY EY NTG G+ T+ RVTW G+ +I +TEA FT +F++G
Sbjct: 246 PAGWFPWDGNFALDTLYYGEYQNTGAGAATSGRVTWKGFKVITSSTEAQGFTPGSFIAGG 305
Query: 552 NWLPQTGVPYNGGF 565
+WL T P++ G
Sbjct: 306 SWLKATTFPFSLGL 319
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 348 bits (893), Expect = 5e-96, Method: Compositional matrix adjust.
Identities = 171/318 (53%), Positives = 211/318 (66%), Gaps = 4/318 (1%)
Query: 249 VIDIVTVALDGTGNFSTITDAINVAPNNTNPDNGYFLIYVTAGVYQEYISIPKNKKNLMM 308
+I VA DGTG++ T+ +A+ AP+ + ++IYV G Y+E + + NK NLM+
Sbjct: 1 IIANAVVAQDGTGDYQTLAEAVAAAPDKSKTR---YVIYVKRGTYKENVEVASNKMNLMI 57
Query: 309 IGDGINQTIITGNRNVVDGWTTSNSATFIVVAPNFVASDITIRNTAGAVKHQAVALRSAA 368
+GDG+ T ITG+ NVVDG TT SAT V F+ DI I+NTAG K QAVALR A
Sbjct: 58 VGDGMYATTITGSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGA 117
Query: 369 DLSTFYSCSFEGYQDTLYTHSLRQFYRECDIYGTVDFIFGNAAVVLQNCNIYPRLPMSGQ 428
D+S C + YQDTLY HS RQFYR+ + GTVDFIFGNAAVV Q C + R P Q
Sbjct: 118 DMSVINRCRIDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKYQ 177
Query: 429 FNAITAQGRTDPNQNTGTSIHNCTIRASNDLASGSQTVQTYLGRPWKEYSRTVYMQTFMD 488
N +TAQGRTDPNQ TGTSI C I AS+DL + TYLGRPWKEYSRTV M++++
Sbjct: 178 QNMVTAQGRTDPNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYLG 237
Query: 489 SLINPAGWHDWSGDFALSTLYYAEYNNTGPGSDTTNRVTWPGYHII-DATEAANFTVSNF 547
LINPAGW +W GDFAL TLYY E+ N GPG+ T+ RV WPGYH+I D +A FTV+
Sbjct: 238 GLINPAGWAEWDGDFALKTLYYGEFMNNGPGAGTSKRVKWPGYHVITDPAKAMPFTVAKL 297
Query: 548 LSGDNWLPQTGVPYNGGF 565
+ G +WL TGV Y G
Sbjct: 298 IQGGSWLRSTGVAYVDGL 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 = 110 bits (276), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 110/341 (32%), Positives = 151/341 (44%), Gaps = 67/341 (19%)
Query: 263 FSTITDAINVAPNNTNPDNGYFLIYVTAGVYQEYISIPKNKKNLMMIGDGINQTIITGNR 322
F TI DAI AP + P F+I + GVY E ++I +N NL + G+ N +I
Sbjct: 18 FKTIADAIASAPAGSTP----FVILIKNGVYNERLTITRN--NLHLKGESRNGAVIAAAT 71
Query: 323 NVV----DG--WTTSNSATFIVVAPNFVASDITIRNT-------------AGAVKH-QAV 362
DG W T+ S+T + A +F A +TIRN + +K QAV
Sbjct: 72 AAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAV 131
Query: 363 AL--RSAADLSTFYSCSFEGYQDTLYTHSLRQFYRECDIYGTVDFIFGNAAVVLQNCNIY 420
AL + D + F S GYQDTLY R F+ +C I GTVDFIFG+ + NC++
Sbjct: 132 ALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLV 191
Query: 421 PRLP---MSGQFNAITAQGRTDPNQNTGTSIHNC-TIRASNDLASGSQTVQTYLGRPWKE 476
R SG + T+ NQ G I N IR S+ + + S LGRPW
Sbjct: 192 SRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVPAKSYG----LGRPWHP 247
Query: 477 YS--------------RTVYMQTFMDSLINPAGWHDWSGD--------FALSTLYYAEYN 514
+ +TV++ T MD+ I GW SG F + EY
Sbjct: 248 TTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPEDSRFFEYK 305
Query: 515 NTGPGSDTTNRVTWPGYHIIDATEAANFTVSNFLSGDNWLP 555
+ G G+ V+ + DA +AA +T S L GD W P
Sbjct: 306 SYGAGA----AVSKDRRQLTDA-QAAEYTQSKVL-GD-WTP 339
>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 = 110 bits (275), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 110/341 (32%), Positives = 151/341 (44%), Gaps = 67/341 (19%)
Query: 263 FSTITDAINVAPNNTNPDNGYFLIYVTAGVYQEYISIPKNKKNLMMIGDGINQTIITGNR 322
F TI DAI AP + P F+I + GVY E ++I +N NL + G+ N +I
Sbjct: 18 FKTIADAIASAPAGSTP----FVILIKNGVYNERLTITRN--NLHLKGESRNGAVIAAAT 71
Query: 323 NVV----DG--WTTSNSATFIVVAPNFVASDITIRNT-------------AGAVKH-QAV 362
DG W T+ S+T + A +F A +TIRN + +K QAV
Sbjct: 72 AAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAV 131
Query: 363 AL--RSAADLSTFYSCSFEGYQDTLYTHSLRQFYRECDIYGTVDFIFGNAAVVLQNCNIY 420
AL + D + F S GYQDTLY R F+ +C I GTVDFIFG+ + NC++
Sbjct: 132 ALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLV 191
Query: 421 PRLP---MSGQFNAITAQGRTDPNQNTGTSIHNC-TIRASNDLASGSQTVQTYLGRPWKE 476
R SG + T+ NQ G I N IR S+ + + S LGRPW
Sbjct: 192 SRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVPAKSYG----LGRPWHP 247
Query: 477 YS--------------RTVYMQTFMDSLINPAGWHDWSGD--------FALSTLYYAEYN 514
+ +TV++ T MD+ I GW SG F + EY
Sbjct: 248 TTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPEDSRFFEYK 305
Query: 515 NTGPGSDTTNRVTWPGYHIIDATEAANFTVSNFLSGDNWLP 555
+ G G+ V+ + DA +AA +T S L GD W P
Sbjct: 306 SYGAGA----TVSKDRRQLTDA-QAAEYTQSKVL-GD-WTP 339
>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 = 107 bits (267), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 109/341 (31%), Positives = 150/341 (43%), Gaps = 67/341 (19%)
Query: 263 FSTITDAINVAPNNTNPDNGYFLIYVTAGVYQEYISIPKNKKNLMMIGDGINQTIITGNR 322
F TI DAI AP + P F+I + GVY E ++I +N NL + G+ N +I
Sbjct: 18 FKTIADAIASAPAGSTP----FVILIKNGVYNERLTITRN--NLHLKGESRNGAVIAAAT 71
Query: 323 NVV----DG--WTTSNSATFIVVAPNFVASDITIRNT-------------AGAVKH-QAV 362
DG W T+ S+T + A +F A +TIRN + +K QAV
Sbjct: 72 AAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAV 131
Query: 363 AL--RSAADLSTFYSCSFEGYQDTLYTHSLRQFYRECDIYGTVDFIFGNAAVVLQNCNIY 420
AL + D + F S GYQ TLY R F+ +C I GTVDFIFG+ + NC++
Sbjct: 132 ALYVTKSGDRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLV 191
Query: 421 PRLPM---SGQFNAITAQGRTDPNQNTGTSIHNC-TIRASNDLASGSQTVQTYLGRPWKE 476
R SG + T+ NQ G I N IR S+ + + S LGRPW
Sbjct: 192 SRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVPAKSYG----LGRPWHP 247
Query: 477 YS--------------RTVYMQTFMDSLINPAGWHDWSGD--------FALSTLYYAEYN 514
+ +TV++ T MD+ I GW SG F + EY
Sbjct: 248 TTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPEDSRFFEYK 305
Query: 515 NTGPGSDTTNRVTWPGYHIIDATEAANFTVSNFLSGDNWLP 555
+ G G+ V+ + DA +AA +T S L GD W P
Sbjct: 306 SYGAGA----TVSKDRRQLTDA-QAAEYTQSKVL-GD-WTP 339
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 102 bits (254), Expect = 6e-22, Method: Compositional matrix adjust.
Identities = 93/306 (30%), Positives = 137/306 (44%), Gaps = 60/306 (19%)
Query: 262 NFSTITDAINVAPNNTNPDNGYFLIYVTAGVYQEYISIPKNKKNLMMIGDGINQTIITGN 321
FS+I A+ AP + P F+I++ GVY E + + ++ ++ + G+ + T+I N
Sbjct: 43 EFSSINAALKSAPKDDTP----FIIFLKNGVYTERLEVARS--HVTLKGENRDGTVIGAN 96
Query: 322 RNVV------DGWTTSNSATFIVVAPNFVASDITIRN----TAGAVKH----------QA 361
+ W TS S+T +V APNF A ++TIRN A K QA
Sbjct: 97 TAAGMLNPQGEKWGTSGSSTVLVNAPNFTAENLTIRNDFDFPANKKKADTDPTKLKDTQA 156
Query: 362 VALRSA--ADLSTFYSCSFEGYQDTLYTHS-LRQFYRECDIYGTVDFIFGNAAVVLQNCN 418
VAL A +D + F + EGYQDTLY+ + R ++ +C+I G VDFIFG+ V NCN
Sbjct: 157 VALLLAENSDKARFKAVKLEGYQDTLYSKTGSRSYFSDCEISGHVDFIFGSGITVFDNCN 216
Query: 419 IYP--RLPMSGQFNAITAQGRTDPNQNTGTSIHNCTIRASNDLASGSQTVQTYLGRPWKE 476
I R + + ITA P+ T + I + G LGRPW
Sbjct: 217 IVARDRSDIEPPYGYITA-----PSTLTTSPYGLIFINSRLTKEPGVPANSFALGRPWHP 271
Query: 477 YS--------------RTVYMQTFMDSLINPAGWHDWSGD--------FALSTLYYAEYN 514
+ ++V++ T MD I GW SG F + E N
Sbjct: 272 TTTFADGRYADPAAIGQSVFINTTMDDHI--YGWDKMSGKDKQGEKIWFYPQDSRFFEAN 329
Query: 515 NTGPGS 520
+ GPG+
Sbjct: 330 SQGPGA 335
>pdb|3GRH|A Chain A, Crystal Structure Of Escherichia Coli Ybhc
Length = 422
Score = 33.5 bits (75), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 29/87 (33%), Positives = 39/87 (44%), Gaps = 16/87 (18%)
Query: 347 DITIRNTAG----AVKHQAVALRSAADLSTFYSCSFEGYQDTLY-THSLRQFYRECD--- 398
++TI NT G A H AVALR+ D + + G Q+T + T+S Q E +
Sbjct: 207 NLTIENTLGDSVDAGNHPAVALRTDGDQVQINNVNILGRQNTFFVTNSGVQNRLETNRQP 266
Query: 399 --------IYGTVDFIFGNAAVVLQNC 417
I G VD + G AVV N
Sbjct: 267 RTLVTNSYIEGDVDIVSGRGAVVFDNT 293
>pdb|3HRK|A Chain A, Histidyl-Trna Synthetase From Trypanosoma Cruzi
(Histidyl-Adenylate Complex)
pdb|3HRK|B Chain B, Histidyl-Trna Synthetase From Trypanosoma Cruzi
(Histidyl-Adenylate Complex)
pdb|3LC0|A Chain A, Histidyl-Trna Synthetase From Trypanosoma Cruzi (Histidine
Complex)
Length = 456
Score = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 4/57 (7%)
Query: 387 THSLRQFYRECDIYGTVDFIFGNAAVVLQ----NCNIYPRLPMSGQFNAITAQGRTD 439
LRQF+ + + YG D++ +A+VV ++ G+F A+ GR D
Sbjct: 265 VKELRQFFEQVEAYGYGDWVLFDASVVRGLAYYTGIVFEGFDREGKFRALCGGGRYD 321
>pdb|1OOP|C Chain C, The Crystal Structure Of Swine Vesicular Disease Virus
Length = 238
Score = 30.0 bits (66), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 31/133 (23%), Positives = 53/133 (39%), Gaps = 22/133 (16%)
Query: 418 NIYPRLPMSGQFNAITAQGRTD---PNQNTG---TSIHNCTIRASNDLASGSQTVQTYLG 471
++ P + + GQ N + D P NT SI I ++ +GSQ G
Sbjct: 29 DVTPEMDIPGQVNNLMEIAEVDSVVPVNNTEGKVMSIEAYQIPVQSNPTNGSQV----FG 84
Query: 472 RPWKEYSRTVYMQTFMDSLINPAGWHDWSGDFALSTLYYAE----------YNNTGPGSD 521
P + +V +T + ++N + WSG L+ ++ Y+ G G+
Sbjct: 85 FPLTPGANSVLNRTLLGEILN--YYAHWSGSIKLTFMFCGSAMATGKFLLAYSPPGAGAP 142
Query: 522 TTNRVTWPGYHII 534
TT + G H+I
Sbjct: 143 TTRKEAMLGTHVI 155
>pdb|1MQT|C Chain C, Swine Vesicular Disease Virus Coat Protein
Length = 238
Score = 30.0 bits (66), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 31/133 (23%), Positives = 53/133 (39%), Gaps = 22/133 (16%)
Query: 418 NIYPRLPMSGQFNAITAQGRTD---PNQNTG---TSIHNCTIRASNDLASGSQTVQTYLG 471
++ P + + GQ N + D P NT SI I ++ +GSQ G
Sbjct: 29 DVTPEMDIPGQVNNLMEIAEVDSVVPVNNTEGKEMSIEAYQIPVQSNPTNGSQV----FG 84
Query: 472 RPWKEYSRTVYMQTFMDSLINPAGWHDWSGDFALSTLYYAE----------YNNTGPGSD 521
P + +V +T + ++N + WSG L+ ++ Y+ G G+
Sbjct: 85 FPLTPGASSVLNRTLLGEILN--YYAHWSGSIKLTFMFCGSAMATGKFLLAYSPPGAGAP 142
Query: 522 TTNRVTWPGYHII 534
TT + G H+I
Sbjct: 143 TTRKEAMLGTHVI 155
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 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,675,194
Number of Sequences: 62578
Number of extensions: 705396
Number of successful extensions: 1498
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1476
Number of HSP's gapped (non-prelim): 15
length of query: 567
length of database: 14,973,337
effective HSP length: 104
effective length of query: 463
effective length of database: 8,465,225
effective search space: 3919399175
effective search space used: 3919399175
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: 54 (25.4 bits)