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= 013167
         (448 letters)

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

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



>pdb|1WJT|A Chain A, Solution Structure Of The N-Terminal Domain I Of Mouse
           Transcription Elongation Factor S-Ii Protein 3
          Length = 103

 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 36/92 (39%), Positives = 54/92 (58%), Gaps = 5/92 (5%)

Query: 138 EVLRIKEILHN--SRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGS-KQI 194
           E+LRI + L    SR +++  L + L++L    +++  L+ T IG AVNG+RKH S K++
Sbjct: 13  ELLRIAKKLEKMVSRKKTEGAL-DLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEV 71

Query: 195 RHLARTLIEGWKDLVDEWVNATKAIAEGTPDS 226
             LA+ LI+ WK L+D     TK   E  P S
Sbjct: 72  VSLAKVLIKNWKRLLDS-PRTTKGERESGPSS 102


>pdb|1VIX|A Chain A, Crystal Structure Of A Putative Peptidase T
 pdb|1VIX|B Chain B, Crystal Structure Of A Putative Peptidase T
          Length = 420

 Score = 29.3 bits (64), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 12/27 (44%), Positives = 17/27 (62%)

Query: 103 CRDDHVSNQIVSNFSSGDIAEALTDEI 129
           C   +V+ QIV N+  GDIA  + DE+
Sbjct: 87  CSGKNVNPQIVENYRGGDIALGIGDEV 113


>pdb|1KSH|A Chain A, Complex Of Arl2 And Pde Delta, Crystal Form 2 (Native)
          Length = 186

 Score = 28.9 bits (63), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 3/41 (7%)

Query: 11  WRNYFRSANGDIFDIIDHAVMVAALDCPKEFK--LRRDRIA 49
           WRNYF S +G I+ ++D A      DC +E +  L  +R+A
Sbjct: 79  WRNYFESTDGLIW-VVDSADRQRMQDCQRELQSLLVEERLA 118


>pdb|1KSJ|A Chain A, Complex Of Arl2 And Pde Delta, Crystal Form 2 (Semet)
          Length = 186

 Score = 28.9 bits (63), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 3/41 (7%)

Query: 11  WRNYFRSANGDIFDIIDHAVMVAALDCPKEFK--LRRDRIA 49
           WRNYF S +G I+ ++D A      DC +E +  L  +R+A
Sbjct: 79  WRNYFESTDGLIW-VVDSADRQRXQDCQRELQSLLVEERLA 118


>pdb|1KSG|A Chain A, Complex Of Arl2 And Pde Delta, Crystal Form 1
          Length = 186

 Score = 28.9 bits (63), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 3/41 (7%)

Query: 11  WRNYFRSANGDIFDIIDHAVMVAALDCPKEFK--LRRDRIA 49
           WRNYF S +G I+ ++D A      DC +E +  L  +R+A
Sbjct: 79  WRNYFESTDGLIW-VVDSADRQRMQDCQRELQSLLVEERLA 118


>pdb|3DOE|A Chain A, Complex Of Arl2 And Bart, Crystal Form 1
 pdb|3DOF|A Chain A, Complex Of Arl2 And Bart, Crystal Form 2
          Length = 192

 Score = 28.9 bits (63), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 3/41 (7%)

Query: 11  WRNYFRSANGDIFDIIDHAVMVAALDCPKEFK--LRRDRIA 49
           WRNYF S +G I+ ++D A      DC +E +  L  +R+A
Sbjct: 77  WRNYFESTDGLIW-VVDSADRQRMQDCQRELQSLLVEERLA 116


>pdb|4GOK|B Chain B, The Crystal Structure Of Arl2gppnhp In Complex With
           Unc119a
 pdb|4GOK|A Chain A, The Crystal Structure Of Arl2gppnhp In Complex With
           Unc119a
          Length = 169

 Score = 28.5 bits (62), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 3/41 (7%)

Query: 11  WRNYFRSANGDIFDIIDHAVMVAALDCPKEFK--LRRDRIA 49
           WRNYF S +G I+ ++D A      DC +E +  L  +R+A
Sbjct: 62  WRNYFESTDGLIW-VVDSADRQRMQDCQRELQSLLVEERLA 101


  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
   0.312    0.130    0.370 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,772,116
Number of Sequences: 62578
Number of extensions: 510847
Number of successful extensions: 962
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 958
Number of HSP's gapped (non-prelim): 9
length of query: 448
length of database: 14,973,337
effective HSP length: 102
effective length of query: 346
effective length of database: 8,590,381
effective search space: 2972271826
effective search space used: 2972271826
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (25.0 bits)