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= psy12242
         (498 letters)

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

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



>pdb|4GBY|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To D-Xylose
 pdb|4GBZ|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To D-Glucose
 pdb|4GC0|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To
           6-Bromo-6-Deoxy-D-Glucose
          Length = 491

 Score =  134 bits (337), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 109/416 (26%), Positives = 204/416 (49%), Gaps = 44/416 (10%)

Query: 109 YVAERFGRKGGLLINNVFVVLAALLQGFSK-AFSSY---------------EMIILGRFL 152
           Y + RFGR+  L I  V   ++ +   + +  F+S                E +I  R +
Sbjct: 77  YCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYVPEFVIY-RII 135

Query: 153 IGINSGLNAGLAPMYLAEISPVHLRGAVGTVYQ--------LVITISIVISQIXXXXXXX 204
            GI  GL + L+PMY+AE++P H+RG + +  Q        LV  ++  I++        
Sbjct: 136 GGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIAR--SGDASW 193

Query: 205 XTADGWPLLLAFTLVPGIYQMITLPFCPESPKYILLSKGQELEAQRALSWLRGTIEVHDE 264
              DGW  + A   +P +  ++ L   PESP++ L+S+G++ +A+  L  + G       
Sbjct: 194 LNTDGWRYMFASECIPALLFLMLLYTVPESPRW-LMSRGKQEQAEGILRKIMGNTLATQA 252

Query: 265 MDEMRAEYESIKLIPKVSLREMFTNAQLRIPLFISMTVMVAQQLSGINAVIYFSTKIFTM 324
           + E++   +  +   K   R +     +   + I + + + QQ  GIN V+Y++ ++F  
Sbjct: 253 VQEIKHSLDHGR---KTGGRLLMFGVGV---IVIGVMLSIFQQFVGINVVLYYAPEVFKT 306

Query: 325 AQLSDTAAQWATLGMGTMNVVMTLVSLVLVEISGRKTLLLIGFMGVFVVTVLLTIVMQFV 384
              S   A   T+ +G +N+  T+++++ V+  GRK L +IG +G+ +    L     + 
Sbjct: 307 LGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAF-YT 365

Query: 385 EIFVMSIFCIILVIMFVVFFAVGPGSIPWFLVSELFSQSARPLATSLAVSINWTANFIVG 444
           +     I  ++ ++ +V  FA+  G + W L+SE+F  + R  A ++AV+  W AN+ V 
Sbjct: 366 Q--APGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVS 423

Query: 445 LGFLPIES----IIH---GYVFTIFAVLQAMFVLFIYKKVPETKNKTQEEIAAMFR 493
             F  ++     + H   G+ + I+  +  +  LF++K VPETK KT EE+ A++ 
Sbjct: 424 WTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEALWE 479


>pdb|1Y9U|A Chain A, Bordetella Ferric Binding Protein
 pdb|2OWS|A Chain A, Crystal Structure Of Bordetella Pertussis Holo Ferric
           Binding Protein Bound With Two Synergistic Oxalate
           Anions
 pdb|2OWT|A Chain A, Crystal Structure Of Bordetella Pertussis Holo Ferric
           Binding Protein With Bound Synergistic Carbonate Anion
          Length = 323

 Score = 31.6 bits (70), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 20/86 (23%), Positives = 40/86 (46%), Gaps = 4/86 (4%)

Query: 112 ERFGRKGGLLINNVFVVLAALLQGFSKAFSSYEMIIL----GRFLIGINSGLNAGLAPMY 167
           + F +  G+ +N VFV    L +  ++   S   +++    G  +  +N G+   +    
Sbjct: 24  DAFAKDSGIKVNTVFVKDGLLERVRAEGDKSPADVLMTVDIGNLIDLVNGGVTQKIQSQT 83

Query: 168 LAEISPVHLRGAVGTVYQLVITISIV 193
           L  + P +LRGA G+ Y L +   ++
Sbjct: 84  LDSVVPANLRGAEGSWYALSLRDRVL 109


>pdb|3ZYY|X Chain X, Reductive Activator For Corrinoid,Iron-Sulfur Protein
 pdb|3ZYY|Y Chain Y, Reductive Activator For Corrinoid,Iron-Sulfur Protein
          Length = 631

 Score = 30.0 bits (66), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 28/95 (29%), Positives = 44/95 (46%), Gaps = 28/95 (29%)

Query: 271 EYESIKLIPKVSLREMFTNAQLRIPLFISMTVMVAQQLSGINAVIYF-----STKIFTMA 325
           EYE +K +P++   E F           S+TV V+  L G+N  +Y      S ++F +A
Sbjct: 163 EYEQLKDLPQILRNENF-----------SVTVGVSDYL-GLNKALYIKSGSASQRVFGLA 210

Query: 326 QLSDTAAQWATLGMGTMNVVMTLVSLVLVEISGRK 360
                      + +GT  VV+ LV LV  ++ G K
Sbjct: 211 -----------IDIGTTTVVVQLVDLVSGKVLGTK 234


  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    0.139    0.399 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,062,313
Number of Sequences: 62578
Number of extensions: 427859
Number of successful extensions: 1114
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1108
Number of HSP's gapped (non-prelim): 3
length of query: 498
length of database: 14,973,337
effective HSP length: 103
effective length of query: 395
effective length of database: 8,527,803
effective search space: 3368482185
effective search space used: 3368482185
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 bits)