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= psy880
         (263 letters)

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

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



>pdb|3ORG|A Chain A, Crystal Structure Of A Eukaryotic Clc Transporter
 pdb|3ORG|B Chain B, Crystal Structure Of A Eukaryotic Clc Transporter
 pdb|3ORG|C Chain C, Crystal Structure Of A Eukaryotic Clc Transporter
 pdb|3ORG|D Chain D, Crystal Structure Of A Eukaryotic Clc Transporter
          Length = 632

 Score = 75.1 bits (183), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 54/161 (33%), Positives = 76/161 (47%), Gaps = 20/161 (12%)

Query: 105 DELRNKYRGRCATKFAAVFRFVWKHTFAKLGEDWVFLALLGIIMATISFFMDXXXXXXXX 164
           +ELR K   R A +FA    +V                  G+ +  +S F          
Sbjct: 36  EELRMKI-SRLAGRFAGYILYVVS----------------GVALCLLSTFWCAVLSTEAE 78

Query: 165 XXXXPEMKTILRGV--ALKEYLTFNTLVAKIIGLTATLGSGLPLGKEGPFVHIASIVATL 222
               P+MK+IL G    ++  L    L AK +GL   +G GLP+G EGP VHIA I+A  
Sbjct: 79  GSGLPQMKSILSGFYDKMRSALELRVLFAKALGLICAIGGGLPVGWEGPNVHIACIIAHQ 138

Query: 223 LSKLVTSFQGIYENESRNSEMLAAACAVGVGSCFGAPIGAT 263
             +L   F+ +  + +   + LAAACAVG+ S FGAP+G  
Sbjct: 139 FYRL-GVFKELCTDRALRLQTLAAACAVGLASSFGAPLGGV 178


>pdb|1KPL|A Chain A, Crystal Structure Of The Clc Chloride Channel From S.
           Typhimurium
 pdb|1KPL|B Chain B, Crystal Structure Of The Clc Chloride Channel From S.
           Typhimurium
 pdb|1KPL|C Chain C, Crystal Structure Of The Clc Chloride Channel From S.
           Typhimurium
 pdb|1KPL|D Chain D, Crystal Structure Of The Clc Chloride Channel From S.
           Typhimurium
          Length = 473

 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 34/123 (27%), Positives = 57/123 (46%), Gaps = 7/123 (5%)

Query: 138 WVFLALLGIIMATISFFMDXXXXXXXXXXXXPEMKTILRGVALKEYLTFNTLVAKIIGLT 197
           W    +L  ++A + +F+             PE++  L    L+    +  L  K IG  
Sbjct: 79  WPLAFILSALLAMVGYFLVRKFAPEAGGSGIPEIEGALE--ELRPVRWWRVLPVKFIGGM 136

Query: 198 ATLGSGLPLGKEGPFVHIASIVATLLSKLVTSFQGIYENESRNSEMLAAACAVGVGSCFG 257
            TLG+G+ LG+EGP V I       L ++V     +   E+R++ +LA   A G+ + F 
Sbjct: 137 GTLGAGMVLGREGPTVQIGGN----LGRMVLDVFRMRSAEARHT-LLATGAAAGLSAAFN 191

Query: 258 API 260
           AP+
Sbjct: 192 APL 194


>pdb|3ND0|A Chain A, X-Ray Crystal Structure Of A Slow Cyanobacterial Cl-H+
           ANTIPORTER
 pdb|3ND0|B Chain B, X-Ray Crystal Structure Of A Slow Cyanobacterial Cl-H+
           ANTIPORTER
 pdb|3Q17|A Chain A, Structure Of A Slow Clc Cl-H+ ANTIPORTER FROM A
           CYANOBACTERIUM IN Bromide
 pdb|3Q17|B Chain B, Structure Of A Slow Clc Cl-H+ ANTIPORTER FROM A
           CYANOBACTERIUM IN Bromide
          Length = 466

 Score = 29.6 bits (65), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 29/124 (23%), Positives = 54/124 (43%), Gaps = 10/124 (8%)

Query: 138 WVFLALLGIIMATISFFMDXXXXXXXXXXXXPEMKTILRGVALKEYLTFN-TLVAKIIGL 196
           W+  AL+   M  +SF++             P+++  L G   K  L +   L  K++G 
Sbjct: 75  WLVTALISGGMVALSFWLMKRFAPDTSGSGIPQIEGHLEG---KLPLVWQRVLPIKLVGG 131

Query: 197 TATLGSGLPLGKEGPFVHIASIVATLLSKLVTSFQGIYENESRNSEMLAAACAVGVGSCF 256
             +LG+G+  G EGP + +   +  +       F+   EN+     ++A     G+ + F
Sbjct: 132 FLSLGAGMLAGFEGPTIQMGGSIGQMTGGW---FKATQENQ---RILIAVGAGAGLATAF 185

Query: 257 GAPI 260
            AP+
Sbjct: 186 NAPL 189


  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
   0.321    0.135    0.406 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,810,348
Number of Sequences: 62578
Number of extensions: 225914
Number of successful extensions: 491
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 468
Number of HSP's gapped (non-prelim): 23
length of query: 263
length of database: 14,973,337
effective HSP length: 97
effective length of query: 166
effective length of database: 8,903,271
effective search space: 1477942986
effective search space used: 1477942986
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: 50 (23.9 bits)