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= psy10473
         (124 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>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 = 59.7 bits (143), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 26/63 (41%), Positives = 41/63 (65%), Gaps = 1/63 (1%)

Query: 20  DSTYHCPQA-SRLHILHMDPSIAVCFLCKTENDFASLCSQIRAELRPEQQPLFELIEDPI 78
           D T+HC Q+  R++IL++DPS+A+ F CK E DF + CS ++ E+  E   +FEL++   
Sbjct: 293 DQTFHCLQSPQRMNILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMFELVQKHP 352

Query: 79  EDW 81
             W
Sbjct: 353 SHW 355


>pdb|2D1I|A Chain A, Structure Of Human Atg4b
 pdb|2D1I|B Chain B, Structure Of Human Atg4b
          Length = 398

 Score = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 36/106 (33%), Positives = 51/106 (48%), Gaps = 12/106 (11%)

Query: 20  DSTYHCPQA-SRLHILHMDPSIAVCFLCKTENDFASLCSQIRA-ELRPEQQPLFELIEDP 77
           D ++HC     R+ I  +DPSIAV F CKTE+DF   C Q++   L     P+FEL+E  
Sbjct: 301 DESFHCQHPPCRMSIAELDPSIAVGFFCKTEDDFNDWCQQVKKLSLLGGALPMFELVEQ- 359

Query: 78  IEDWTPTQPRPSNLGGTSSPSCSSMRRQPRRVSGVGEGSDDDFEFL 123
                    +PS+L      + S       R+    +  D+DFE L
Sbjct: 360 ---------QPSHLACPDVLNLSLDSSDVERLERFFDSEDEDFEIL 396


>pdb|2CY7|A Chain A, The Crystal Structure Of Human Atg4b
          Length = 396

 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 36/106 (33%), Positives = 51/106 (48%), Gaps = 12/106 (11%)

Query: 20  DSTYHCPQA-SRLHILHMDPSIAVCFLCKTENDFASLCSQIRA-ELRPEQQPLFELIEDP 77
           D ++HC     R+ I  +DPSIAV F CKTE+DF   C Q++   L     P+FEL+E  
Sbjct: 299 DESFHCQHPPCRMSIAELDPSIAVGFFCKTEDDFNDWCQQVKKLSLLGGALPMFELVEQ- 357

Query: 78  IEDWTPTQPRPSNLGGTSSPSCSSMRRQPRRVSGVGEGSDDDFEFL 123
                    +PS+L      + S       R+    +  D+DFE L
Sbjct: 358 ---------QPSHLACPDVLNLSLDSSDVERLERFFDSEDEDFEIL 394


>pdb|2ZZP|A Chain A, The Crystal Structure Of Human Atg4b(C74s)- Lc3(1-124)
           Complex
          Length = 357

 Score = 52.0 bits (123), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 26/58 (44%), Positives = 35/58 (60%), Gaps = 2/58 (3%)

Query: 20  DSTYHCPQA-SRLHILHMDPSIAVCFLCKTENDFASLCSQIRA-ELRPEQQPLFELIE 75
           D ++HC     R+ I  +DPSIAV F CKTE+DF   C Q++   L     P+FEL+E
Sbjct: 299 DESFHCQHPPCRMSIAELDPSIAVGFFCKTEDDFNDWCQQVKKLSLLGGALPMFELVE 356


>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 = 52.0 bits (123), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 26/58 (44%), Positives = 35/58 (60%), Gaps = 2/58 (3%)

Query: 20  DSTYHCPQA-SRLHILHMDPSIAVCFLCKTENDFASLCSQIRA-ELRPEQQPLFELIE 75
           D ++HC     R+ I  +DPSIAV F CKTE+DF   C Q++   L     P+FEL+E
Sbjct: 299 DESFHCQHPPCRMSIAELDPSIAVGFFCKTEDDFNDWCQQVKKLSLLGGALPMFELVE 356


>pdb|1NMN|A Chain A, Structure Of Yqgf From Escherichia Coli, A Hypothetical
           Protein
 pdb|1NMN|B Chain B, Structure Of Yqgf From Escherichia Coli, A Hypothetical
           Protein
          Length = 138

 Score = 26.9 bits (58), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 3/46 (6%)

Query: 69  PLFELIEDPIEDWTPTQ---PRPSNLGGTSSPSCSSMRRQPRRVSG 111
           P + +IE  +++W P +     P N+ GT  P  +  R+   R+ G
Sbjct: 40  PDWNIIERLLKEWQPDEIIVGLPLNMDGTEQPLTARARKFANRIHG 85


>pdb|1OVQ|A Chain A, Solution Structure Of The Hypothetical Protein Yqgf From
           Escherichia Coli
          Length = 138

 Score = 26.6 bits (57), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 3/46 (6%)

Query: 69  PLFELIEDPIEDWTPTQ---PRPSNLGGTSSPSCSSMRRQPRRVSG 111
           P + +IE  +++W P +     P N+ GT  P  +  R+   R+ G
Sbjct: 40  PDWNIIERLLKEWQPDEIIVGLPLNMDGTEQPLTARARKFANRIHG 85


>pdb|3MLQ|A Chain A, Crystal Structure Of The Thermus Thermophilus
          Transcription-Repair Coupling Factor Rna Polymerase
          Interacting Domain With The Thermus Aquaticus Rna
          Polymerase Beta1 Domain
 pdb|3MLQ|B Chain B, Crystal Structure Of The Thermus Thermophilus
          Transcription-Repair Coupling Factor Rna Polymerase
          Interacting Domain With The Thermus Aquaticus Rna
          Polymerase Beta1 Domain
 pdb|3MLQ|C Chain C, Crystal Structure Of The Thermus Thermophilus
          Transcription-Repair Coupling Factor Rna Polymerase
          Interacting Domain With The Thermus Aquaticus Rna
          Polymerase Beta1 Domain
 pdb|3MLQ|D Chain D, Crystal Structure Of The Thermus Thermophilus
          Transcription-Repair Coupling Factor Rna Polymerase
          Interacting Domain With The Thermus Aquaticus Rna
          Polymerase Beta1 Domain
          Length = 188

 Score = 26.2 bits (56), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 10/28 (35%), Positives = 16/28 (57%)

Query: 13 QDSEKKLDSTYHCPQASRLHILHMDPSI 40
          QD  ++ D TY  P  +RL ++H D  +
Sbjct: 65 QDECREKDLTYQAPLYARLQLIHKDTGL 92


>pdb|1IW7|C Chain C, Crystal Structure Of The Rna Polymerase Holoenzyme From
           Thermus Thermophilus At 2.6a Resolution
 pdb|1IW7|M Chain M, Crystal Structure Of The Rna Polymerase Holoenzyme From
           Thermus Thermophilus At 2.6a Resolution
 pdb|1SMY|C Chain C, Structural Basis For Transcription Regulation By Alarmone
           Ppgpp
 pdb|1SMY|M Chain M, Structural Basis For Transcription Regulation By Alarmone
           Ppgpp
 pdb|1ZYR|C Chain C, Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Streptolydigin
 pdb|1ZYR|M Chain M, Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Streptolydigin
 pdb|2A68|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifabutin
 pdb|2A68|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifabutin
 pdb|2A69|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifapentin
 pdb|2A69|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifapentin
 pdb|2A6E|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme
 pdb|2A6E|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme
 pdb|2A6H|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Sterptolydigin
 pdb|2A6H|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Sterptolydigin
 pdb|2CW0|C Chain C, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme At 3.3 Angstroms Resolution
 pdb|2CW0|M Chain M, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme At 3.3 Angstroms Resolution
 pdb|2BE5|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Inhibitor Tagetitoxin
 pdb|2BE5|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Inhibitor Tagetitoxin
 pdb|2O5I|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Elongation Complex
 pdb|2O5I|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Elongation Complex
 pdb|2O5J|C Chain C, Crystal Structure Of The T. Thermophilus Rnap Polymerase
           Elongation Complex With The Ntp Substrate Analog
 pdb|2O5J|M Chain M, Crystal Structure Of The T. Thermophilus Rnap Polymerase
           Elongation Complex With The Ntp Substrate Analog
 pdb|2PPB|C Chain C, Crystal Structure Of The T. Thermophilus Rnap Polymerase
           Elongation Complex With The Ntp Substrate Analog And
           Antibiotic Streptolydigin
 pdb|2PPB|M Chain M, Crystal Structure Of The T. Thermophilus Rnap Polymerase
           Elongation Complex With The Ntp Substrate Analog And
           Antibiotic Streptolydigin
 pdb|3DXJ|C Chain C, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Myxopyronin
 pdb|3DXJ|M Chain M, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Myxopyronin
 pdb|3EQL|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Myxopyronin
 pdb|3EQL|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Myxopyronin
 pdb|3AOH|C Chain C, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
 pdb|3AOH|H Chain H, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
 pdb|3AOH|M Chain M, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
 pdb|3AOI|C Chain C, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
 pdb|3AOI|H Chain H, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
 pdb|3AOI|M Chain M, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
 pdb|4G7H|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
           Initiation Complex
 pdb|4G7H|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
           Initiation Complex
 pdb|4G7O|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
           Initiation Complex Containing 2 Nt Of Rna
 pdb|4G7O|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
           Initiation Complex Containing 2 Nt Of Rna
 pdb|4G7Z|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
           Initiation Complex Containing 5-Bru At Template-Strand
           Position +1
 pdb|4G7Z|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
           Initiation Complex Containing 5-Bru At Template-Strand
           Position +1
 pdb|4GZY|C Chain C, Crystal Structures Of Bacterial Rna Polymerase Paused
           Elongation Complexes
 pdb|4GZZ|C Chain C, Crystal Structures Of Bacterial Rna Polymerase Paused
           Elongation Complexes
          Length = 1119

 Score = 25.4 bits (54), Expect = 8.3,   Method: Composition-based stats.
 Identities = 10/28 (35%), Positives = 16/28 (57%)

Query: 13  QDSEKKLDSTYHCPQASRLHILHMDPSI 40
           QD  ++ D TY  P  +RL ++H D  +
Sbjct: 80  QDECREKDLTYQAPLYARLQLIHKDTGL 107


>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
          Length = 1118

 Score = 25.4 bits (54), Expect = 8.3,   Method: Composition-based stats.
 Identities = 10/28 (35%), Positives = 16/28 (57%)

Query: 13  QDSEKKLDSTYHCPQASRLHILHMDPSI 40
           QD  ++ D TY  P  +RL ++H D  +
Sbjct: 80  QDECREKDLTYQAPLYARLQLIHKDTGL 107


>pdb|1HQM|C Chain C, Crystal Structure Of Thermus Aquaticus Core Rna
           Polymerase- Includes Complete Structure With Side-Chains
           (Except For Disordered Regions)-Further Refined From
           Original Deposition-Contains Additional Sequence
           Information
          Length = 1119

 Score = 25.4 bits (54), Expect = 8.3,   Method: Composition-based stats.
 Identities = 10/28 (35%), Positives = 16/28 (57%)

Query: 13  QDSEKKLDSTYHCPQASRLHILHMDPSI 40
           QD  ++ D TY  P  +RL ++H D  +
Sbjct: 80  QDECREKDLTYQAPLYARLQLIHKDTGL 107


>pdb|1L9U|C Chain C, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 pdb|1L9U|L Chain L, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 pdb|1L9Z|C Chain C, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
           Promoter Dna Complex At 6.5 A Resolution
          Length = 1118

 Score = 25.4 bits (54), Expect = 8.3,   Method: Composition-based stats.
 Identities = 10/28 (35%), Positives = 16/28 (57%)

Query: 13  QDSEKKLDSTYHCPQASRLHILHMDPSI 40
           QD  ++ D TY  P  +RL ++H D  +
Sbjct: 80  QDECREKDLTYQAPLYARLQLIHKDTGL 107


>pdb|1YNJ|C Chain C, Taq Rna Polymerase-Sorangicin Complex
 pdb|1YNN|C Chain C, Taq Rna Polymerase-rifampicin Complex
 pdb|2GHO|C Chain C, Recombinant Thermus Aquaticus Rna Polymerase For
           Structural Studies
          Length = 1119

 Score = 25.4 bits (54), Expect = 8.5,   Method: Composition-based stats.
 Identities = 10/28 (35%), Positives = 16/28 (57%)

Query: 13  QDSEKKLDSTYHCPQASRLHILHMDPSI 40
           QD  ++ D TY  P  +RL ++H D  +
Sbjct: 80  QDECREKDLTYQAPLYARLQLIHKDTGL 107


  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
   0.316    0.135    0.417 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,126,925
Number of Sequences: 62578
Number of extensions: 158536
Number of successful extensions: 270
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 259
Number of HSP's gapped (non-prelim): 13
length of query: 124
length of database: 14,973,337
effective HSP length: 85
effective length of query: 39
effective length of database: 9,654,207
effective search space: 376514073
effective search space used: 376514073
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)