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= 036608
         (565 letters)

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

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



>pdb|3UYJ|A Chain A, Crystal Structure Of Jmjd5 Catalytic Core Domain In
           Complex With Nickle And Alpha-Kg
 pdb|3UYJ|B Chain B, Crystal Structure Of Jmjd5 Catalytic Core Domain In
           Complex With Nickle And Alpha-Kg
          Length = 248

 Score = 30.4 bits (67), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 7/63 (11%)

Query: 505 NHFIEVFMLPASPI--PPIANSWIKYHEPCAEGWATPYKTNIIAFKDLVFEVTTQETIDL 562
            HF E F++P  P+    +A+ W     PC + W+  Y   I   + +  EV ++ T + 
Sbjct: 25  QHFREQFLVPGRPVILKGVADHW-----PCMQKWSLEYIQEIAGCRTVPVEVGSRYTDEE 79

Query: 563 ASQ 565
            SQ
Sbjct: 80  WSQ 82


>pdb|2D2R|A Chain A, Crystal Structure Of Helicobacter Pylori Undecaprenyl
           Pyrophosphate Synthase
 pdb|2D2R|B Chain B, Crystal Structure Of Helicobacter Pylori Undecaprenyl
           Pyrophosphate Synthase
 pdb|2DTN|A Chain A, Crystal Structure Of Helicobacter Pylori Undecaprenyl
           Pyrophosphate Synthase Complexed With Pyrophosphate
 pdb|2DTN|B Chain B, Crystal Structure Of Helicobacter Pylori Undecaprenyl
           Pyrophosphate Synthase Complexed With Pyrophosphate
          Length = 245

 Score = 30.4 bits (67), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 23/88 (26%), Positives = 39/88 (44%), Gaps = 12/88 (13%)

Query: 352 MSVSQTKAPKHASYIDSFPFGLRPYICGVSDVVADGNCGFRAVANLIGIGEDSWAQVRKD 411
            S    K PK  S +D     L+ Y+        D N  FRA+ +L G  ++      +D
Sbjct: 68  FSTENWKRPK--SEVDFLMKMLKKYLKDERSTYLDNNIRFRAIGDLEGFSKE-----LRD 120

Query: 412 LVIELQS---HFNDYKRV--FEYAGRAE 434
            +++L++   HF D+ +V    Y  + E
Sbjct: 121 TILQLENDTRHFKDFTQVLALNYGSKNE 148


>pdb|4AAP|A Chain A, Crystal Structure Of Jmjd5 Domain Of Human Lysine-Specific
           Demethylase 8 (Kdm8) In Complex With N-Oxalylglycine
           (Nog)
 pdb|4AAP|B Chain B, Crystal Structure Of Jmjd5 Domain Of Human Lysine-Specific
           Demethylase 8 (Kdm8) In Complex With N-Oxalylglycine
           (Nog)
          Length = 239

 Score = 30.0 bits (66), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 7/63 (11%)

Query: 505 NHFIEVFMLPASPI--PPIANSWIKYHEPCAEGWATPYKTNIIAFKDLVFEVTTQETIDL 562
            HF E F++P  P+    +A+ W     PC + W+  Y   I   + +  EV ++ T + 
Sbjct: 16  QHFREQFLVPGRPVILKGVADHW-----PCMQKWSLEYIQEIAGCRTVPVEVGSRYTDEE 70

Query: 563 ASQ 565
            SQ
Sbjct: 71  WSQ 73


>pdb|4GJY|A Chain A, Jmjd5 In Complex With N-Oxalylglycine
          Length = 235

 Score = 30.0 bits (66), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 7/63 (11%)

Query: 505 NHFIEVFMLPASPI--PPIANSWIKYHEPCAEGWATPYKTNIIAFKDLVFEVTTQETIDL 562
            HF E F++P  P+    +A+ W     PC + W+  Y   I   + +  EV ++ T + 
Sbjct: 12  QHFREQFLVPGRPVILKGVADHW-----PCXQKWSLEYIQEIAGCRTVPVEVGSRYTDEE 66

Query: 563 ASQ 565
            SQ
Sbjct: 67  WSQ 69


>pdb|4GJZ|A Chain A, Jmjd5 In Complex With 2-Oxoglutarate
          Length = 235

 Score = 30.0 bits (66), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 7/63 (11%)

Query: 505 NHFIEVFMLPASPI--PPIANSWIKYHEPCAEGWATPYKTNIIAFKDLVFEVTTQETIDL 562
            HF E F++P  P+    +A+ W     PC + W+  Y   I   + +  EV ++ T + 
Sbjct: 12  QHFREQFLVPGRPVILKGVADHW-----PCMQKWSLEYIQEIAGCRTVPVEVGSRYTDEE 66

Query: 563 ASQ 565
            SQ
Sbjct: 67  WSQ 69


>pdb|3QHA|A Chain A, Crystal Structure Of A Putative Oxidoreductase From
           Mycobacterium Avium 104
 pdb|3QHA|B Chain B, Crystal Structure Of A Putative Oxidoreductase From
           Mycobacterium Avium 104
          Length = 296

 Score = 30.0 bits (66), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 31/68 (45%), Gaps = 7/68 (10%)

Query: 168 IKASFEKSLTTVQHSFTPSVFKELRGLVARNALDMILSES-----KRANLIGIDISACGC 222
           IK +F+     V H+  P     ++  +ARN L      +     K A   G+D+ A G 
Sbjct: 157 IKPAFKHWAAVVIHAGEPGAGTRMK--LARNMLTFTSYAAACEAMKLAEAAGLDLQALGR 214

Query: 223 VVRHTHGL 230
           VVRHT  L
Sbjct: 215 VVRHTDAL 222


  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
   0.320    0.133    0.402 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,327,613
Number of Sequences: 62578
Number of extensions: 659235
Number of successful extensions: 1437
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1436
Number of HSP's gapped (non-prelim): 7
length of query: 565
length of database: 14,973,337
effective HSP length: 104
effective length of query: 461
effective length of database: 8,465,225
effective search space: 3902468725
effective search space used: 3902468725
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: 54 (25.4 bits)