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= 013221
         (447 letters)

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

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



>pdb|3BHS|A Chain A, Nitrosomonas Europaea Rh50 And Mechanism Of Conduction By
           Rhesus Protein Family Of Channels
          Length = 406

 Score = 30.0 bits (66), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 53/240 (22%), Positives = 92/240 (38%), Gaps = 43/240 (17%)

Query: 3   FWTFFEVASMPIVQV------LLISVLGALMATQYWNLLTADARRSLNKMVFTVFTPSLM 56
           FW  F  A +P  Q+       L+++ GA +AT + + L    + S+  M        + 
Sbjct: 189 FWPSFATAIVPFEQMPQTIVNTLLALCGATLATYFLSALFHKGKASIVDMANAALAGGVA 248

Query: 57  FASLAKTVTLEEIISWWFMPVNVAMTFLIGGILGWIVVKLLRPKPHLEGLVIATCASGNL 116
             S+   V           PV   +  L+GG +  +    ++P    +   I TC   NL
Sbjct: 249 IGSVCNIVG----------PVGAFVIGLLGGAISVVGFVFIQPMLESKAKTIDTCGVHNL 298

Query: 117 GNLL--------LIIVPAICHEQGSPFGNRDVCSSVGLSYASFSMALGGFFIWSYSYQL- 167
             L         ++IVP I   Q          + +G++ A   +AL G  I     +L 
Sbjct: 299 HGLPGLLGGFSAILIVPGIAVAQ---------LTGIGITLA---LALIGGVIAGALIKLT 346

Query: 168 --IKQSSVRYKALAQAAEPEEVPKEVNKDFDANAQTQLLRGTTDDQEDVSVLVASTKSSS 225
              KQ+          A PE+  K      +A  + Q L+    ++ D +VL A ++ ++
Sbjct: 347 GTTKQAYEDSHEFIHLAGPEDEHKAERLVLEAKTEIQGLK----NRIDAAVLSAKSEGNA 402


>pdb|3B9W|A Chain A, The 1.3 A Resolution Structure Of Nitrosomonas Europaea
           Rh50 And Mechanistic Implications For Nh3 Transport By
           Rhesus Family Proteins
          Length = 407

 Score = 29.3 bits (64), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 53/238 (22%), Positives = 90/238 (37%), Gaps = 43/238 (18%)

Query: 3   FWTFFEVASMPIVQV------LLISVLGALMATQYWNLLTADARRSLNKMVFTVFTPSLM 56
           FW  F  A +P  Q+       L+++ GA +AT + + L    + S+  M        + 
Sbjct: 190 FWPSFATAIVPFEQMPQTIVNTLLALCGATLATYFLSALFHKGKASIVDMANAALAGGVA 249

Query: 57  FASLAKTVTLEEIISWWFMPVNVAMTFLIGGILGWIVVKLLRPKPHLEGLVIATCASGNL 116
             S+   V           PV   +  L+GG +  +    ++P    +   I TC   NL
Sbjct: 250 IGSVCNIVG----------PVGAFVIGLLGGAISVVGFVFIQPMLESKAKTIDTCGVHNL 299

Query: 117 GNLL--------LIIVPAICHEQGSPFGNRDVCSSVGLSYASFSMALGGFFIWSYSYQL- 167
             L         ++IVP I   Q          + +G++ A   +AL G  I     +L 
Sbjct: 300 HGLPGLLGGFSAILIVPGIAVAQ---------LTGIGITLA---LALIGGVIAGALIKLT 347

Query: 168 --IKQSSVRYKALAQAAEPEEVPKEVNKDFDANAQTQLLRGTTDDQEDVSVLVASTKS 223
              KQ+          A PE+  K      +A  + Q L+    ++ D +VL A ++ 
Sbjct: 348 GTTKQAYEDSHEFIHLAGPEDEHKAERLVLEAKTEIQGLK----NRIDAAVLSAKSEG 401


>pdb|1XOC|A Chain A, The Structure Of The Oligopeptide-Binding Protein, Appa,
           From Bacillus Subtilis In Complex With A Nonapeptide
          Length = 520

 Score = 28.9 bits (63), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 11/81 (13%)

Query: 109 ATCASGNL--GNLLLIIVPAICHEQGSPFGNRDVCSSVGLSYASFSMALGGFFIWSYSYQ 166
           A  A   L  G++    VPA  ++    F N  + + + LSY         +  W+   +
Sbjct: 225 ANAAEAQLQAGDINFFNVPATDYKTAEKFNNLKIVTDLALSYV--------YIGWNEKNE 276

Query: 167 LIKQSSVRYKALAQAAEPEEV 187
           L K   VR +AL  A + E +
Sbjct: 277 LFKDKKVR-QALTTALDRESI 296


>pdb|3B9Y|A Chain A, Crystal Structure Of The Nitrosomonas Europaea Rh Protein
 pdb|3B9Z|A Chain A, Crystal Structure Of The Nitrosomonas Europaea Rh Protein
           Complexed With Carbon Dioxide
          Length = 388

 Score = 28.5 bits (62), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 50/224 (22%), Positives = 82/224 (36%), Gaps = 39/224 (17%)

Query: 3   FWTFFEVASMPIVQV------LLISVLGALMATQYWNLLTADARRSLNKMVFTVFTPSLM 56
           FW  F  A +P  Q+       L+++ GA +AT + + L    + S+  M        + 
Sbjct: 184 FWPSFATAIVPFEQMPQTIVNTLLALCGATLATYFLSALFHKGKASIVDMANAALAGGVA 243

Query: 57  FASLAKTVTLEEIISWWFMPVNVAMTFLIGGILGWIVVKLLRPKPHLEGLVIATCASGNL 116
             S+   V           PV   +  L+GG +  +    ++P    +   I TC   NL
Sbjct: 244 IGSVCNIVG----------PVGAFVIGLLGGAISVVGFVFIQPMLESKAKTIDTCGVHNL 293

Query: 117 GNLL--------LIIVPAICHEQGSPFGNRDVCSSVGLSYASFSMALGGFFIWSYSYQL- 167
             L         ++IVP I   Q          + +G++ A   +AL G  I     +L 
Sbjct: 294 HGLPGLLGGFSAILIVPGIAVAQ---------LTGIGITLA---LALIGGVIAGALIKLT 341

Query: 168 --IKQSSVRYKALAQAAEPEEVPKEVNKDFDANAQTQLLRGTTD 209
              KQ+          A PE+  K      +A  + Q L+   D
Sbjct: 342 GTTKQAYEDSHEFIHLAGPEDEHKAERLVLEAKTEIQGLKNRID 385


  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
   0.326    0.138    0.432 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,604,655
Number of Sequences: 62578
Number of extensions: 424623
Number of successful extensions: 1102
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1101
Number of HSP's gapped (non-prelim): 6
length of query: 447
length of database: 14,973,337
effective HSP length: 102
effective length of query: 345
effective length of database: 8,590,381
effective search space: 2963681445
effective search space used: 2963681445
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 bits)