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= 013664
         (438 letters)

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

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



>pdb|2A3L|A Chain A, X-Ray Structure Of Adenosine 5'-Monophosphate Deaminase
           From Arabidopsis Thaliana In Complex With Coformycin
           5'-Phosphate
          Length = 701

 Score =  675 bits (1741), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 324/388 (83%), Positives = 353/388 (90%), Gaps = 3/388 (0%)

Query: 1   MTDSSKLDTTYLLTNGNAGPNLPDHMNVNAEAIAASSMIRSHSVSGDLHGVQPDPIAADI 60
           +T+S  LD +YL  NG+    +P   N    ++AASSMIRSHSVSGDLHGVQPDPIAADI
Sbjct: 25  LTNSEGLDASYLQANGDN--EMPADANEEQISMAASSMIRSHSVSGDLHGVQPDPIAADI 82

Query: 61  LRKEPEQETFARLQITPKEVPSPDEMEAYVVLQECLEMRKRYLFREAVAPWEKEMISDPS 120
           LRKEPEQETF RL + P EVP+ DE+EAY  LQECLE+RKRY+F+E VAPWEKE+ISDPS
Sbjct: 83  LRKEPEQETFVRLNV-PLEVPTSDEVEAYKCLQECLELRKRYVFQETVAPWEKEVISDPS 141

Query: 121 TPKPNPDPFYYAPVGKSDHHFEMQDGVIHVYPNKDSKEELYPVADATTFFTDLHHILRVI 180
           TPKPN +PF + P GKSDH FEMQDGV+HV+ NKD+KE+L+PVADAT FFTDLHH+L+VI
Sbjct: 142 TPKPNTEPFAHYPQGKSDHCFEMQDGVVHVFANKDAKEDLFPVADATAFFTDLHHVLKVI 201

Query: 181 ALGNMRTLCHHRLLLLEQKFNLHLMLNADKEFLAQKSAPHRDFYNVRKVDTHVHHSACMN 240
           A GN+RTLCH RL+LLEQKFNLHLMLNADKEFLAQKSAPHRDFYNVRKVDTHVHHSACMN
Sbjct: 202 AAGNIRTLCHRRLVLLEQKFNLHLMLNADKEFLAQKSAPHRDFYNVRKVDTHVHHSACMN 261

Query: 241 QKHLLRFIKSKLRKEPDEVVIFRDGTYLTLKEVFESLDLTGYDLNVDLLDVHADKSTFHR 300
           QKHLLRFIKSKLRKEPDEVVIFRDGTYLTL+EVFESLDLTGYDLNVDLLDVHADKSTFHR
Sbjct: 262 QKHLLRFIKSKLRKEPDEVVIFRDGTYLTLREVFESLDLTGYDLNVDLLDVHADKSTFHR 321

Query: 301 FDKFNLKYNPCGQSRLREIFLKQDNLIQGRFLAELTKQVFSDLEASKYQMAEYRISIYGR 360
           FDKFNLKYNPCGQSRLREIFLKQDNLIQGRFL E+TKQVFSDLEASKYQMAEYRISIYGR
Sbjct: 322 FDKFNLKYNPCGQSRLREIFLKQDNLIQGRFLGEITKQVFSDLEASKYQMAEYRISIYGR 381

Query: 361 KQSEWDQLASWIVNNELYSENVVWLIQV 388
           K SEWDQLASWIVNN+LYSENVVWLIQ+
Sbjct: 382 KMSEWDQLASWIVNNDLYSENVVWLIQL 409


>pdb|1YUA|A Chain A, C-Terminal Domain Of Escherichia Coli Topoisomerase I
          Length = 122

 Score = 30.0 bits (66), Expect = 2.6,   Method: Composition-based stats.
 Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 5/72 (6%)

Query: 115 MISDPSTPKPNPDPFYYAPVGKSDHHFEMQDGVIHVYPNKD----SKEELYPVADATTFF 170
           M  + + PK +P P    P  KSD +F ++DG   V+   +    S+E   P+ +    F
Sbjct: 1   MNGEVAPPKEDPVPLPELPCEKSDAYFVLRDGAAGVFLAANTFPKSRETRAPLVEELYRF 60

Query: 171 TD-LHHILRVIA 181
            D L   LR +A
Sbjct: 61  RDRLPEKLRYLA 72


>pdb|3K8P|C Chain C, Structural Basis For Vesicle Tethering By The Dsl1 Complex
          Length = 357

 Score = 28.9 bits (63), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 19/66 (28%), Positives = 37/66 (56%), Gaps = 7/66 (10%)

Query: 281 GYD--LNVDLLDVHADKSTFHR-----FDKFNLKYNPCGQSRLREIFLKQDNLIQGRFLA 333
           G+D  L++D+ +V    S F +     F +F    +  G+S++  I+L + NL+Q  F A
Sbjct: 82  GWDEELDIDVDNVPIQVSVFVQSAAKVFTEFEQGCDTIGRSKVESIYLYKFNLLQTAFFA 141

Query: 334 ELTKQV 339
            ++++V
Sbjct: 142 XVSEKV 147


>pdb|3FC6|B Chain B, Hrxralpha & Mlxralpha With An Indole Pharmacophore,
          Sb786875
 pdb|3FC6|D Chain D, Hrxralpha & Mlxralpha With An Indole Pharmacophore,
          Sb786875
 pdb|3FAL|B Chain B, Humanrxr Alpha & Mouse Lxr Alpha Complexed With Retenoic
          Acid And Gsk2186
 pdb|3FAL|D Chain D, Humanrxr Alpha & Mouse Lxr Alpha Complexed With Retenoic
          Acid And Gsk2186
          Length = 266

 Score = 28.5 bits (62), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 2/61 (3%)

Query: 12 LLTNGNAGPNL-PDHMNVNAEAIAASSMIRSHSVSGDLHGVQPDPIAADILRKEPEQETF 70
          L+  G+  P L P+ + +  + +AA       S S  L  V P PIA D   +E  Q+ F
Sbjct: 15 LVPRGSVLPQLSPEQLGMIEKLVAAQQQCNRRSFSDRLR-VTPWPIAPDPQSREARQQRF 73

Query: 71 A 71
          A
Sbjct: 74 A 74


  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
   0.322    0.136    0.419 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,151,608
Number of Sequences: 62578
Number of extensions: 587934
Number of successful extensions: 1501
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1497
Number of HSP's gapped (non-prelim): 4
length of query: 438
length of database: 14,973,337
effective HSP length: 102
effective length of query: 336
effective length of database: 8,590,381
effective search space: 2886368016
effective search space used: 2886368016
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)