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= 013429
(443 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2D1I|A Chain A, Structure Of Human Atg4b
pdb|2D1I|B Chain B, Structure Of Human Atg4b
Length = 398
Score = 182 bits (463), Expect = 2e-46, Method: Compositional matrix adjust.
Identities = 107/330 (32%), Positives = 159/330 (48%), Gaps = 25/330 (7%)
Query: 100 DFSSRILISYRKGFDPIGDSKITSDVGWGCMLRSSQMLVAQALLFHRLGRPWRKPLQKPF 159
D +SR+ +YRK F IG + TSD GWGCMLR QM+ AQAL+ LGR WR +K
Sbjct: 50 DVASRLWFTYRKNFPAIGGTGPTSDTGWGCMLRCGQMIFAQALVCRHLGRDWRWTQRKRQ 109
Query: 160 DREYVEILHLFGDSETSPFSIHNLLQAGKAYGLAAGSWVGPYAMCRSWEALARCQRAETG 219
Y +L+ F D + S +SIH + Q G G + G W GP + + + LA +
Sbjct: 110 PDSYFSVLNAFIDRKDSYYSIHQIAQMGVGEGKSIGQWYGPNTVAQVLKKLAVFDTWSS- 168
Query: 220 LGCQSLPMAIYV-----VSGDEDGERGGAPVVCID------DASRHCSVFSKGQ------ 262
+A+++ V +E V C D+ RHC+ F G
Sbjct: 169 -------LAVHIAMDNTVVMEEIRRLCRTSVPCAGATAFPADSDRHCNGFPAGAEVTNRP 221
Query: 263 ADWTPIXXXXXXXXXXEKVNPRYIPTLRLTFTFPQSLGIVGGKPGASTYIVGVQEESAIY 322
+ W P+ +N Y+ TL+ F PQSLG++GGKP ++ Y +G E IY
Sbjct: 222 SPWRPLVLLIPLRLGLTDINEAYVETLKHCFMMPQSLGVIGGKPNSAHYFIGYVGEELIY 281
Query: 323 LDPHDVQPVINIGKDDLEADTSTYHSDVIRHIHLDSIDPSLAIGFYCRDKDDFDDFCARA 382
LDPH QP + D S + + + +DPS+A+GF+C+ +DDF+D+C +
Sbjct: 282 LDPHTTQPAVEPTDGCFIPDESFHCQHPPCRMSIAELDPSIAVGFFCKTEDDFNDWCQQV 341
Query: 383 SKLAEESNGAPLFTVTQTHKKPVNHSDVLG 412
KL+ P+F + + + DVL
Sbjct: 342 KKLSLLGGALPMFELVEQQPSHLACPDVLN 371
>pdb|2CY7|A Chain A, The Crystal Structure Of Human Atg4b
Length = 396
Score = 182 bits (463), Expect = 3e-46, Method: Compositional matrix adjust.
Identities = 107/330 (32%), Positives = 159/330 (48%), Gaps = 25/330 (7%)
Query: 100 DFSSRILISYRKGFDPIGDSKITSDVGWGCMLRSSQMLVAQALLFHRLGRPWRKPLQKPF 159
D +SR+ +YRK F IG + TSD GWGCMLR QM+ AQAL+ LGR WR +K
Sbjct: 48 DVASRLWFTYRKNFPAIGGTGPTSDTGWGCMLRCGQMIFAQALVCRHLGRDWRWTQRKRQ 107
Query: 160 DREYVEILHLFGDSETSPFSIHNLLQAGKAYGLAAGSWVGPYAMCRSWEALARCQRAETG 219
Y +L+ F D + S +SIH + Q G G + G W GP + + + LA +
Sbjct: 108 PDSYFSVLNAFIDRKDSYYSIHQIAQMGVGEGKSIGQWYGPNTVAQVLKKLAVFDTWSS- 166
Query: 220 LGCQSLPMAIYV-----VSGDEDGERGGAPVVCID------DASRHCSVFSKGQ------ 262
+A+++ V +E V C D+ RHC+ F G
Sbjct: 167 -------LAVHIAMDNTVVMEEIRRLCRTSVPCAGATAFPADSDRHCNGFPAGAEVTNRP 219
Query: 263 ADWTPIXXXXXXXXXXEKVNPRYIPTLRLTFTFPQSLGIVGGKPGASTYIVGVQEESAIY 322
+ W P+ +N Y+ TL+ F PQSLG++GGKP ++ Y +G E IY
Sbjct: 220 SPWRPLVLLIPLRLGLTDINEAYVETLKHCFMMPQSLGVIGGKPNSAHYFIGYVGEELIY 279
Query: 323 LDPHDVQPVINIGKDDLEADTSTYHSDVIRHIHLDSIDPSLAIGFYCRDKDDFDDFCARA 382
LDPH QP + D S + + + +DPS+A+GF+C+ +DDF+D+C +
Sbjct: 280 LDPHTTQPAVEPTDGCFIPDESFHCQHPPCRMSIAELDPSIAVGFFCKTEDDFNDWCQQV 339
Query: 383 SKLAEESNGAPLFTVTQTHKKPVNHSDVLG 412
KL+ P+F + + + DVL
Sbjct: 340 KKLSLLGGALPMFELVEQQPSHLACPDVLN 369
>pdb|2Z0D|A Chain A, The Crystal Structure Of Human Atg4b- Lc3(1-120) Complex
pdb|2Z0E|A Chain A, The Crystal Structure Of Human Atg4b- Lc3(1-124) Complex
Length = 357
Score = 176 bits (447), Expect = 2e-44, Method: Compositional matrix adjust.
Identities = 103/317 (32%), Positives = 154/317 (48%), Gaps = 25/317 (7%)
Query: 100 DFSSRILISYRKGFDPIGDSKITSDVGWGCMLRSSQMLVAQALLFHRLGRPWRKPLQKPF 159
D +SR+ +YRK F IG + TSD GWGCMLR QM+ AQAL+ LGR WR +K
Sbjct: 48 DVASRLWFTYRKNFPAIGGTGPTSDTGWGCMLRCGQMIFAQALVCRHLGRDWRWTQRKRQ 107
Query: 160 DREYVEILHLFGDSETSPFSIHNLLQAGKAYGLAAGSWVGPYAMCRSWEALARCQRAETG 219
Y +L+ F D + S +SIH + Q G G + G W GP + + + LA +
Sbjct: 108 PDSYFSVLNAFIDRKDSYYSIHQIAQMGVGEGKSIGQWYGPNTVAQVLKKLAVFDTWSS- 166
Query: 220 LGCQSLPMAIYV-----VSGDEDGERGGAPVVCID------DASRHCSVFSKGQ------ 262
+A+++ V +E V C D+ RHC+ F G
Sbjct: 167 -------LAVHIAMDNTVVMEEIRRLCRTSVPCAGATAFPADSDRHCNGFPAGAEVTNRP 219
Query: 263 ADWTPIXXXXXXXXXXEKVNPRYIPTLRLTFTFPQSLGIVGGKPGASTYIVGVQEESAIY 322
+ W P+ +N Y+ TL+ F PQSLG++GGKP ++ Y +G E IY
Sbjct: 220 SPWRPLVLLIPLRLGLTDINEAYVETLKHCFMMPQSLGVIGGKPNSAHYFIGYVGEELIY 279
Query: 323 LDPHDVQPVINIGKDDLEADTSTYHSDVIRHIHLDSIDPSLAIGFYCRDKDDFDDFCARA 382
LDP QP + D S + + + +DPS+A+GF+C+ +DDF+D+C +
Sbjct: 280 LDPATTQPAVEPTDGCFIPDESFHCQHPPCRMSIAELDPSIAVGFFCKTEDDFNDWCQQV 339
Query: 383 SKLAEESNGAPLFTVTQ 399
KL+ P+F + +
Sbjct: 340 KKLSLLGGALPMFELVE 356
>pdb|2ZZP|A Chain A, The Crystal Structure Of Human Atg4b(C74s)- Lc3(1-124)
Complex
Length = 357
Score = 176 bits (447), Expect = 2e-44, Method: Compositional matrix adjust.
Identities = 103/317 (32%), Positives = 154/317 (48%), Gaps = 25/317 (7%)
Query: 100 DFSSRILISYRKGFDPIGDSKITSDVGWGCMLRSSQMLVAQALLFHRLGRPWRKPLQKPF 159
D +SR+ +YRK F IG + TSD GWG MLR QM+ AQAL+ LGR WR +K
Sbjct: 48 DVASRLWFTYRKNFPAIGGTGPTSDTGWGSMLRCGQMIFAQALVCRHLGRDWRWTQRKRQ 107
Query: 160 DREYVEILHLFGDSETSPFSIHNLLQAGKAYGLAAGSWVGPYAMCRSWEALARCQRAETG 219
Y +L+ F D + S +SIH + Q G G + G W GP + + + LA +
Sbjct: 108 PDSYFSVLNAFIDRKDSYYSIHQIAQMGVGEGKSIGQWYGPNTVAQVLKKLAVFDTWSS- 166
Query: 220 LGCQSLPMAIYV-----VSGDEDGERGGAPVVCID------DASRHCSVFSKGQ------ 262
+A+++ V +E V C D+ RHC+ F G
Sbjct: 167 -------LAVHIAMDNTVVMEEIRRLCRTSVPCAGATAFPADSDRHCNGFPAGAEVTNRP 219
Query: 263 ADWTPIXXXXXXXXXXEKVNPRYIPTLRLTFTFPQSLGIVGGKPGASTYIVGVQEESAIY 322
+ W P+ +N Y+ TL+ F PQSLG++GGKP ++ Y +G E IY
Sbjct: 220 SPWRPLVLLIPLRLGLTDINEAYVETLKHCFMMPQSLGVIGGKPNSAHYFIGYVGEELIY 279
Query: 323 LDPHDVQPVINIGKDDLEADTSTYHSDVIRHIHLDSIDPSLAIGFYCRDKDDFDDFCARA 382
LDPH QP + D S + + + +DPS+A+GF+C+ +DDF+D+C +
Sbjct: 280 LDPHTTQPAVEPTDGCFIPDESFHCQHPPCRMSIAELDPSIAVGFFCKTEDDFNDWCQQV 339
Query: 383 SKLAEESNGAPLFTVTQ 399
KL+ P+F + +
Sbjct: 340 KKLSLLGGALPMFELVE 356
>pdb|2P82|A Chain A, Cysteine Protease Atg4a
pdb|2P82|B Chain B, Cysteine Protease Atg4a
pdb|2P82|C Chain C, Cysteine Protease Atg4a
pdb|2P82|D Chain D, Cysteine Protease Atg4a
Length = 355
Score = 176 bits (445), Expect = 3e-44, Method: Compositional matrix adjust.
Identities = 98/316 (31%), Positives = 158/316 (50%), Gaps = 22/316 (6%)
Query: 100 DFSSRILISYRKGFDPIGDSKITSDVGWGCMLRSSQMLVAQALLFHRLGRPWRKPLQKPF 159
D S+R+ +YR+ F PIG + +SD GWGCMLR QM++AQAL+ LGR W QK
Sbjct: 44 DISARLWFTYRRKFSPIGGTGPSSDAGWGCMLRCGQMMLAQALICRHLGRDWSWEKQKEQ 103
Query: 160 DREYVEILHLFGDSETSPFSIHNLLQAGKAYGLAAGSWVGP---------YAMCRSWEAL 210
+EY IL F D + +SIH + Q G G + G W GP A+ W +L
Sbjct: 104 PKEYQRILQCFLDRKDCCYSIHQMAQMGVGEGKSIGEWFGPNTVAQVLKKLALFDEWNSL 163
Query: 211 ARCQRAETGLGCQSLPMAIYV--VSGDEDGERGGAPVVCIDDA---SRHCSVFSKGQADW 265
A + + + + V +S D G+R + + + S +CS W
Sbjct: 164 AVYVSMDNTVVIEDIKKMCRVLPLSADTAGDRPPDSLTASNQSKGTSAYCSA-------W 216
Query: 266 TPIXXXXXXXXXXEKVNPRYIPTLRLTFTFPQSLGIVGGKPGASTYIVGVQEESAIYLDP 325
P+ ++NP Y+ + F PQSLG +GGKP + Y +G + I+LDP
Sbjct: 217 KPLLLIVPLRLGINQINPVYVDAFKECFKMPQSLGALGGKPNNAYYFIGFLGDELIFLDP 276
Query: 326 HDVQPVINIGKDDLEADTSTYHSDVIRHIHLDSIDPSLAIGFYCRDKDDFDDFCARASKL 385
H Q ++ ++ D + + + +++ ++DPS+A+GF+C+++ DFD++C+ K
Sbjct: 277 HTTQTFVDTEENGTVNDQTFHCLQSPQRMNILNLDPSVALGFFCKEEKDFDNWCSLVQKE 336
Query: 386 AEESNGAPLFTVTQTH 401
+ N +F + Q H
Sbjct: 337 ILKEN-LRMFELVQKH 351
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 0.135 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,127,106
Number of Sequences: 62578
Number of extensions: 525678
Number of successful extensions: 948
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 934
Number of HSP's gapped (non-prelim): 10
length of query: 443
length of database: 14,973,337
effective HSP length: 102
effective length of query: 341
effective length of database: 8,590,381
effective search space: 2929319921
effective search space used: 2929319921
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: 53 (25.0 bits)