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= 025056
         (258 letters)

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

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



>pdb|2EBM|A Chain A, Solution Structure Of The Rwd Domain Of Human Rwd Domain
           Containing Protein 1
          Length = 128

 Score = 79.7 bits (195), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 49/128 (38%), Positives = 76/128 (59%), Gaps = 11/128 (8%)

Query: 1   MTDHVQEQEMEIEALEAILMDEFKEIHSGESGLNTSNQCFQVTLSPQDDEADESTMPPVE 60
           MTD+ +EQ  E+EALE+I  D F       + L+ +   F +T++ +  E DE+    V+
Sbjct: 8   MTDYGEEQRNELEALESIYPDSF-------TVLSENPPSFTITVTSEAGENDET----VQ 56

Query: 61  LALIFSHTEKYPDEPPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTSAKE 120
             L F+++EKYPDE PL  + S   ++  D+  + + L  +A ENLGM MI+TLVT+ +E
Sbjct: 57  TTLKFTYSEKYPDEAPLYEIFSQENLEDNDVSDILKLLALQAEENLGMVMIFTLVTAVQE 116

Query: 121 WLSERYSQ 128
            L+E   Q
Sbjct: 117 KLNEIVDQ 124


>pdb|1UKX|A Chain A, Solution Structure Of The Rwd Domain Of Mouse Gcn2
          Length = 137

 Score = 50.4 bits (119), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 34/119 (28%), Positives = 58/119 (48%), Gaps = 3/119 (2%)

Query: 6   QEQEMEIEALEAILMDEFKEIHSGESGLNTSNQCFQVTLSPQDDEADESTMPPVELALIF 65
           Q Q+ E++ALEAI   +F+++     G         + L PQ    +E     V++ L  
Sbjct: 13  QRQDHELQALEAIYGSDFQDLRPDARGRVREPPEINLVLYPQGLAGEEVY---VQVELRV 69

Query: 66  SHTEKYPDEPPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTSAKEWLSE 124
                YPD  P +++K+ +G+    + +LK  LE+ A +  G  MI+ L    + +LSE
Sbjct: 70  KCPPTYPDVVPEIDLKNAKGLSNESVNLLKSHLEELAKKQCGEVMIFELAHHVQSFLSE 128


>pdb|2DAY|A Chain A, Solution Structure Of The Rwd Domain Of Human Ring Finger
           Protein 25
          Length = 128

 Score = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 35/113 (30%), Positives = 54/113 (47%), Gaps = 5/113 (4%)

Query: 11  EIEALEAILMDEFKEIHSGESGLNTSNQCFQVTLSPQDDEADESTMPPVELALIFSHTEK 70
           E+E LE+I +DE + I        TS     +TL P   E  +S    V   L+     +
Sbjct: 16  EVEVLESIYLDELQVIKGNG---RTSPWEIYITLHPATAEDQDSQY--VCFTLVLQVPAE 70

Query: 71  YPDEPPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTSAKEWLS 123
           YP E P +++++ RG+    +  + + L   A   LG AM+Y L+   KE LS
Sbjct: 71  YPHEVPQISIRNPRGLSDEQIHTILQVLGHVAKAGLGTAMLYELIEKGKEILS 123


>pdb|2DMF|A Chain A, An Extended Conformation Of The Rwd Domain Of Human Ring
           Finger Protein 25
          Length = 137

 Score = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 34/115 (29%), Positives = 56/115 (48%), Gaps = 5/115 (4%)

Query: 11  EIEALEAILMDEFKEIHSGESGLNTSNQCFQVTLSPQDDEADESTMPPVELALIFSHTEK 70
           E+E LE+I +DE + I   +    TS     +TL P   E  +S    V   L+     +
Sbjct: 16  EVEVLESIYLDELQVI---KGNGRTSPWEIYITLHPATAEDQDSQY--VCFTLVLQVPAE 70

Query: 71  YPDEPPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTSAKEWLSER 125
           YP E P +++++ RG+    +  + + L   A   LG AM+Y L+   KE L++ 
Sbjct: 71  YPHEVPQISIRNPRGLSDEQIHTILQVLGHVAKAGLGTAMLYELIEKGKEILTDN 125


>pdb|2YZ0|A Chain A, Solution Structure Of RwdGI DOMAIN OF SACCHAROMYCES
           Cerevisiae Gcn2
          Length = 138

 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 31/115 (26%), Positives = 61/115 (53%), Gaps = 6/115 (5%)

Query: 11  EIEALEAILMDEFKEIHSGESGLNTSNQ-CFQVTLSPQDDEADESTMPPVELALIFSHTE 69
           E+EA+ +I MD+F ++   +S  +   Q  F++TL   D E  ES+     + L F+ T 
Sbjct: 18  ELEAIRSIYMDDFTDLTKRKSSWDKQPQIIFEITLRSVDKEPVESS-----ITLHFAMTP 72

Query: 70  KYPDEPPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTSAKEWLSE 124
            YP   P +  K+++ +    L++LK + ++  + + G  +I+ + +  +E L E
Sbjct: 73  MYPYTAPEIEFKNVQNVMDSQLQMLKSEFKKIHNTSRGQEIIFEITSFTQEKLDE 127


>pdb|1Z3D|A Chain A, Protein Crystal Growth Improvement Leading To The 2.5a
           Crystallographic Structure Of Ubiquitin-Conjugating
           Enzyme (Ubc-1) From Caenorhabditis Elegans
          Length = 157

 Score = 28.9 bits (63), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 48/108 (44%), Gaps = 14/108 (12%)

Query: 19  LMDEFKEIH----SGESGLNTSNQCF---QVTLSPQDDEADESTMPPVELALIFSHTEKY 71
           LM +FK++     +G SG  T +       +   PQ+   ++ T    +L+L F  TE+Y
Sbjct: 12  LMRDFKKLQEDPPAGVSGAPTEDNILTWEAIIFGPQETPFEDGTF---KLSLEF--TEEY 66

Query: 72  PDEPPLLNV--KSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTS 117
           P++PP +    K        D  I  + L+   S    +A I T + S
Sbjct: 67  PNKPPTVKFISKMFHPNVYADGSICLDILQNRWSPTYDVAAILTSIQS 114


>pdb|1Q34|A Chain A, Crystal Structures Of Two Ubc (E2) Enzymes Of The
           Ubiquitin- Conjugating System In Caenorhabditis Elegans
 pdb|1Q34|B Chain B, Crystal Structures Of Two Ubc (E2) Enzymes Of The
           Ubiquitin- Conjugating System In Caenorhabditis Elegans
 pdb|1Q34|C Chain C, Crystal Structures Of Two Ubc (E2) Enzymes Of The
           Ubiquitin- Conjugating System In Caenorhabditis Elegans
          Length = 163

 Score = 28.1 bits (61), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 48/108 (44%), Gaps = 14/108 (12%)

Query: 19  LMDEFKEIH----SGESGLNTSNQCF---QVTLSPQDDEADESTMPPVELALIFSHTEKY 71
           LM +FK++     +G SG  T +       +   PQ+   ++ T    +L+L F  TE+Y
Sbjct: 9   LMRDFKKLQEDPPAGVSGAPTEDNILTWEAIIFGPQETPFEDGTF---KLSLEF--TEEY 63

Query: 72  PDEPPLLNV--KSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTS 117
           P++PP +    K        D  I  + L+   S    +A I T + S
Sbjct: 64  PNKPPTVKFISKMFHPNVYADGSICLDILQNRWSPTYDVAAILTSIQS 111


  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
   0.307    0.125    0.340 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,217,540
Number of Sequences: 62578
Number of extensions: 206624
Number of successful extensions: 493
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 485
Number of HSP's gapped (non-prelim): 10
length of query: 258
length of database: 14,973,337
effective HSP length: 97
effective length of query: 161
effective length of database: 8,903,271
effective search space: 1433426631
effective search space used: 1433426631
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 50 (23.9 bits)