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= 000819
         (1268 letters)

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

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



>pdb|3GKH|A Chain A, Npc1(ntd)
 pdb|3GKI|A Chain A, Npc1(Ntd):cholesterol
 pdb|3GKJ|A Chain A, Npc1d(ntd):25hydroxycholesterol
          Length = 232

 Score =  107 bits (267), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 74/223 (33%), Positives = 105/223 (47%), Gaps = 19/223 (8%)

Query: 53  CAMYDICGARSDRKVLNCPYNIPSVKPDDLLSSKVQSLCPTI---TGNVCCTEDQFDTLR 109
           C  Y  CG     K  NC Y+ P           VQ LCP       ++CC   Q  TL+
Sbjct: 5   CVWYGECGIAYGDKRYNCEYSGPPKPLPKDGYDLVQELCPGFFFGQVSLCCDVRQLQTLK 64

Query: 110 TQVQQAIPFLVGCPACLRNFLNLFCELTCSPNQSLFINVTS----VSKVSNN--LTVDGI 163
             +Q  + FL  CP+C  N LNLFCELTCSP QS F+ VT+    V  V+N     V  +
Sbjct: 65  DNLQLPLQFLSRCPSCFYNLLNLFCELTCSPRQSQFLQVTATEDYVDPVTNQTKTNVKEL 124

Query: 164 DYYITDTFGQGLYESCKDVKFGTMNTRALDFIGG---GAQNFKDWFAFIGRRAAANLPGS 220
            YY+  +F   +Y +C+DV+  + N +AL  + G    A    +W  ++  +       +
Sbjct: 125 QYYVGQSFANAMYNACRDVEAPSSNDKALGLLCGKDADACQATNWIEYMFNKDNGQ---A 181

Query: 221 PYTIKFWPSAPELSGMIPMNVSAYSCADG----SLGCSCGDCT 259
           P+TI    S   + GM PMN +   C +     +  CSC DC+
Sbjct: 182 PFTITPVFSDFPVHGMEPMNNATKGCDESVDEVTAPCSCQDCS 224


>pdb|3QNT|A Chain A, Npc1l1 (Ntd) Structure
          Length = 265

 Score = 91.7 bits (226), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 78/249 (31%), Positives = 108/249 (43%), Gaps = 33/249 (13%)

Query: 48  HVEEFCAMYDICGARSDRKV-------LNCPYNIPSVK--PDDLLSSKVQSLCPTI-TG- 96
           H   +CA YD CG   +          ++C  N P+ K   D L+   +Q +CP + TG 
Sbjct: 9   HQPGYCAFYDECGKNPELSGSLMTLSNVSCLSNTPARKITGDHLI--LLQKICPRLYTGP 66

Query: 97  --NVCCTEDQFDTLRTQVQQAIPFLVGCPACLRNFLNLFCELTCSPNQSLFINVTSVSKV 154
               CC+  Q  +L   +      L  CPAC  NF+NL C  TCSPNQSLFINVT V+++
Sbjct: 67  NTQACCSAKQLVSLEASLSITKALLTRCPACSDNFVNLHCHNTCSPNQSLFINVTRVAQL 126

Query: 155 SNNL--TVDGIDYYITDTFGQGLYESCKDVKFGTMNTRALDFI----GGGAQNFKDWFAF 208
                  V   + +   +F +  Y+SC  V+     T A+  +    G    N + W  F
Sbjct: 127 GAGQLPAVVAYEAFYQHSFAEQSYDSCSRVRVPAAATLAVGTMCGVYGSALCNAQRWLNF 186

Query: 209 IGRRAAANLPGSPYTIKFW---PSAPELSGMIPMNVSAYSC----ADGSLGCSCGDCTSS 261
            G         +P  I F    P     SG+ P+N     C     D    CSC DC +S
Sbjct: 187 QGDTGNGL---APLDITFHLLEPGQAVGSGIQPLNEGVARCNESQGDDVATCSCQDCAAS 243

Query: 262 PVCSSTAPP 270
             C + A P
Sbjct: 244 --CPAIARP 250


>pdb|2V50|A Chain A, The Missing Part Of The Bacterial Mexab-Oprm System:
            Structural Determination Of The Multidrug Exporter Mexb
 pdb|2V50|B Chain B, The Missing Part Of The Bacterial Mexab-Oprm System:
            Structural Determination Of The Multidrug Exporter Mexb
 pdb|2V50|C Chain C, The Missing Part Of The Bacterial Mexab-Oprm System:
            Structural Determination Of The Multidrug Exporter Mexb
 pdb|2V50|D Chain D, The Missing Part Of The Bacterial Mexab-Oprm System:
            Structural Determination Of The Multidrug Exporter Mexb
 pdb|2V50|E Chain E, The Missing Part Of The Bacterial Mexab-Oprm System:
            Structural Determination Of The Multidrug Exporter Mexb
 pdb|2V50|F Chain F, The Missing Part Of The Bacterial Mexab-Oprm System:
            Structural Determination Of The Multidrug Exporter Mexb
          Length = 1052

 Score = 30.0 bits (66), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 16/72 (22%), Positives = 39/72 (54%)

Query: 1099 NLAIAIGAVFVVCLITTCSFWSSAIILLVLTMIVVDLMGVMAILKIQLNAVSVVNLVMAV 1158
             L  AI  VF+V  +   +F ++ I  + + ++++   GV+A     +N +++  +V+A+
Sbjct: 343  TLGEAILLVFLVMYLFLQNFRATLIPTIAVPVVLLGTFGVLAAFGFSINTLTMFGMVLAI 402

Query: 1159 GIAVEFCVHITH 1170
            G+ V+  + +  
Sbjct: 403  GLLVDDAIVVVE 414


  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
   0.323    0.136    0.410 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 32,541,635
Number of Sequences: 62578
Number of extensions: 1224880
Number of successful extensions: 2220
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 2191
Number of HSP's gapped (non-prelim): 25
length of query: 1268
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1158
effective length of database: 8,089,757
effective search space: 9367938606
effective search space used: 9367938606
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 57 (26.6 bits)