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= 017893
         (364 letters)

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

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



>pdb|3VQI|A Chain A, Crystal Structure Of Kluyveromyces Marxianus Atg5
 pdb|3VQI|B Chain B, Crystal Structure Of Kluyveromyces Marxianus Atg5
 pdb|3VQI|C Chain C, Crystal Structure Of Kluyveromyces Marxianus Atg5
 pdb|3VQI|D Chain D, Crystal Structure Of Kluyveromyces Marxianus Atg5
 pdb|3VQI|E Chain E, Crystal Structure Of Kluyveromyces Marxianus Atg5
          Length = 274

 Score = 30.8 bits (68), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 33/137 (24%), Positives = 57/137 (41%), Gaps = 20/137 (14%)

Query: 165 QGEPLTNAERKAL-VEKCHRNRTKRQINLGRDGLTHNMLNDIHNH-WKHA------EAVR 216
           QG  L +   +   ++ CH ++  R I    DG  H+ + D   H WK A       A R
Sbjct: 103 QGNELDDTSLQMWELQLCHGDKYPRGILPLVDG--HSQIKDYWRHQWKQACFILNGSAKR 160

Query: 217 IKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEP 276
           I  L +P  D +N         +  I+ R+    +  R + ++  K   +P+ +W  +  
Sbjct: 161 IMSLSIP--DFENF--------WVSILSRNRSDFMAVRSKLFSMNKAKSLPVRVWTSNYA 210

Query: 277 VYPKLIKTTIEGLSIEE 293
           V    +  T + LS+ E
Sbjct: 211 VLQPTVPVTDKELSVAE 227


>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Mn
 pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Ca
          Length = 501

 Score = 30.8 bits (68), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 39/82 (47%), Gaps = 10/82 (12%)

Query: 158 ILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRI 217
           IL + R+ G P T  + +AL+EK          N G    T    ND   +W +A AV  
Sbjct: 365 ILHKSRVNGGPATYPKNRALLEKWK--------NAGALYATPPGSND-DWYWLYA-AVSC 414

Query: 218 KCLGVPTVDMKNVCFQLEDKTF 239
           KCL V   +M++  FQL   +F
Sbjct: 415 KCLLVTNDEMRDHLFQLLGNSF 436


>pdb|1JO0|A Chain A, Structure Of Hi1333, A Hypothetical Protein From
           Haemophilus Influenzae With Structural Similarity To
           Rna-binding Proteins
 pdb|1JO0|B Chain B, Structure Of Hi1333, A Hypothetical Protein From
           Haemophilus Influenzae With Structural Similarity To
           Rna-binding Proteins
          Length = 98

 Score = 30.4 bits (67), Expect = 1.5,   Method: Composition-based stats.
 Identities = 19/65 (29%), Positives = 31/65 (47%)

Query: 190 INLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGT 249
           + LG +GLT  +L +I N   H E +++K  G      + +   +  +T    +   G  
Sbjct: 22  VMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTIGHI 81

Query: 250 LVLYR 254
           LVLYR
Sbjct: 82  LVLYR 86


>pdb|4G23|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Mn
 pdb|4G25|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana, Semet Substituted Form With Sr
          Length = 501

 Score = 28.5 bits (62), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 27/82 (32%), Positives = 38/82 (46%), Gaps = 10/82 (12%)

Query: 158 ILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRI 217
           IL + R+ G P T  + +AL+EK          N G    T    ND   +W +A AV  
Sbjct: 365 ILHKSRVNGGPATYPKNRALLEKWK--------NAGALYATPPGSND-DWYWLYA-AVSC 414

Query: 218 KCLGVPTVDMKNVCFQLEDKTF 239
           KCL V   + ++  FQL   +F
Sbjct: 415 KCLLVTNDEXRDHLFQLLGNSF 436


>pdb|3RPD|A Chain A, The Structure Of A B12-Independent Methionine Synthase
           From Shewanella Sp. W3-18-1 In Complex With
           Selenomethionine.
 pdb|3RPD|B Chain B, The Structure Of A B12-Independent Methionine Synthase
           From Shewanella Sp. W3-18-1 In Complex With
           Selenomethionine
          Length = 357

 Score = 28.1 bits (61), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 11/22 (50%), Positives = 17/22 (77%)

Query: 271 WRPHEPVYPKLIKTTIEGLSIE 292
           WR +E V+PKL K+ I+ +S+E
Sbjct: 245 WRQYEEVFPKLQKSNIDIISLE 266


  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
   0.321    0.139    0.426 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,865,108
Number of Sequences: 62578
Number of extensions: 399363
Number of successful extensions: 827
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 823
Number of HSP's gapped (non-prelim): 8
length of query: 364
length of database: 14,973,337
effective HSP length: 100
effective length of query: 264
effective length of database: 8,715,537
effective search space: 2300901768
effective search space used: 2300901768
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)