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= 018975
         (348 letters)

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

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



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

 Score = 37.7 bits (86), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 26/107 (24%), Positives = 48/107 (44%), Gaps = 4/107 (3%)

Query: 17  YGDECVVLD----SYPPHLHLRIKPRTADVSSQQFVEAVIGIRASPKYPEHPPRIDLIES 72
           Y DE  V+     + P  +++ + P TA+    Q+V   + ++   +YP   P+I +   
Sbjct: 24  YLDELQVIKGNGRTSPWEIYITLHPATAEDQDSQYVCFTLVLQVPAEYPHEVPQISIRNP 83

Query: 73  KGLDDQRQKHLISCIQDKAHELTSCLMLVALCEEAVAKLSAMNHPDG 119
           +GL D++   ++  +   A       ML  L E+    L+  N P G
Sbjct: 84  RGLSDEQIHTILQVLGHVAKAGLGTAMLYELIEKGKEILTDNNIPHG 130


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

 Score = 36.2 bits (82), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 23/88 (26%), Positives = 44/88 (50%), Gaps = 1/88 (1%)

Query: 28  PPHLHLRIKPRTADVSSQQFVEAVIGIRASPKYPEHPPRIDLIESKGLDDQRQKHLISCI 87
           PP ++L + P+      + +V+  + ++  P YP+  P IDL  +KGL ++    L S +
Sbjct: 44  PPEINLVLYPQGL-AGEEVYVQVELRVKCPPTYPDVVPEIDLKNAKGLSNESVNLLKSHL 102

Query: 88  QDKAHELTSCLMLVALCEEAVAKLSAMN 115
           ++ A +    +M+  L     + LS  N
Sbjct: 103 EELAKKQCGEVMIFELAHHVQSFLSEHN 130


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

 Score = 35.4 bits (80), Expect = 0.041,   Method: Compositional matrix adjust.
 Identities = 20/98 (20%), Positives = 40/98 (40%), Gaps = 2/98 (2%)

Query: 17  YGDECVVLDSYPPHLHLRIKPRTADVSSQQFVEAVIGIRASPKYPEHPPRIDLIESKGLD 76
           Y D   VL   PP   + +     +  + + V+  +    S KYP+  P  ++   + L+
Sbjct: 26  YPDSFTVLSENPPSFTITVTSEAGE--NDETVQTTLKFTYSEKYPDEAPLYEIFSQENLE 83

Query: 77  DQRQKHLISCIQDKAHELTSCLMLVALCEEAVAKLSAM 114
           D     ++  +  +A E    +M+  L      KL+ +
Sbjct: 84  DNDVSDILKLLALQAEENLGMVMIFTLVTAVQEKLNEI 121


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

 Score = 35.0 bits (79), Expect = 0.060,   Method: Compositional matrix adjust.
 Identities = 24/101 (23%), Positives = 45/101 (44%), Gaps = 4/101 (3%)

Query: 17  YGDECVVLD----SYPPHLHLRIKPRTADVSSQQFVEAVIGIRASPKYPEHPPRIDLIES 72
           Y DE  V+     + P  +++ + P TA+    Q+V   + ++   +YP   P+I +   
Sbjct: 24  YLDELQVIKGNGRTSPWEIYITLHPATAEDQDSQYVCFTLVLQVPAEYPHEVPQISIRNP 83

Query: 73  KGLDDQRQKHLISCIQDKAHELTSCLMLVALCEEAVAKLSA 113
           +GL D++   ++  +   A       ML  L E+    LS 
Sbjct: 84  RGLSDEQIHTILQVLGHVAKAGLGTAMLYELIEKGKEILSG 124


>pdb|2PFX|A Chain A, Crystal Structure Of Uncharacterized Peroxidase-related
           Protein (yp_614459.1) From Silicibacter Sp. Tm1040 At
           1.70 A Resolution
 pdb|2PFX|B Chain B, Crystal Structure Of Uncharacterized Peroxidase-related
           Protein (yp_614459.1) From Silicibacter Sp. Tm1040 At
           1.70 A Resolution
          Length = 191

 Score = 28.9 bits (63), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 23/90 (25%), Positives = 38/90 (42%), Gaps = 4/90 (4%)

Query: 61  PEHPPRIDLIESKGLDDQRQKHLISCIQDKAHELTSCLMLVALCEEAVAKLSAMNHPDGD 120
           P+ P  +DL  +  L D+ QK+   C Q+K   + + L   A     V KL+A      D
Sbjct: 5   PKEPTALDLPXADPLPDETQKYFEIC-QEKLGXVPNVLKAYAFN---VEKLNAFTAXYND 60

Query: 121 CPLCLYPLFRKDKNVEVLPFMKLMSCFHCF 150
             L    L + ++    +    +  CF+C 
Sbjct: 61  LXLGESQLSKLEREXIAVVVSSINKCFYCL 90


  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
   0.319    0.135    0.423 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,506,079
Number of Sequences: 62578
Number of extensions: 364620
Number of successful extensions: 877
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 868
Number of HSP's gapped (non-prelim): 12
length of query: 348
length of database: 14,973,337
effective HSP length: 100
effective length of query: 248
effective length of database: 8,715,537
effective search space: 2161453176
effective search space used: 2161453176
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)