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= 042477
         (478 letters)

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

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



>pdb|2XUT|A Chain A, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter.
 pdb|2XUT|B Chain B, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter.
 pdb|2XUT|C Chain C, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter
          Length = 524

 Score = 53.1 bits (126), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 95/478 (19%), Positives = 173/478 (36%), Gaps = 72/478 (15%)

Query: 5   ERFAFKGVASNLVTYLTDVMKMS-----NSSAAKTV-SSWNGLTSMXXXXXXXXXDSYWD 58
           ERF+F G+ + L  +L   + +S       + AK V  S+               D ++ 
Sbjct: 24  ERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIGVYFFPLLGGWIADRFFG 83

Query: 59  RHSTILAFSFIYVLGLMALTSTAFAWAESPANTTXXXXXXXXXXXXXXXXXAGYNPSLQA 118
           +++TIL  S IY +G   L           A                     G  P + +
Sbjct: 84  KYNTILWLSLIYCVGHAFL-----------AIFEHSVQGFYTGLFLIALGSGGIKPLVSS 132

Query: 119 FGADQMDNNNDDEEILPCTLDNQXXXXXXXXXXXXXWWYFGVCSGSLLGITLMSYIQDTF 178
           F  DQ D +N  + +     D                +YF +  GS      M  +   F
Sbjct: 133 FMGDQFDQSN--KSLAQKAFDM---------------FYFTINFGSFFASLSMPLLLKNF 175

Query: 179 GWVIGFAIPTIAMLXXXXXXXXXXRFCKKKSDHEALKNKPFMSIVQAIKVAASKLKNGKA 238
           G  + F IP + M              +K+  H   + K     +  I+ A      GK 
Sbjct: 176 GAAVAFGIPGVLMFVATVFFW----LGRKRYIHMPPEPKDPHGFLPVIRSALLTKVEGKG 231

Query: 239 ----ISPIDKSDAMELELQEKP-------LCCN--------DQNKELDDELENPKNVKHA 279
               +  +    +    L   P       LCC              L  E     +   A
Sbjct: 232 NIGLVLALIGGVSAAYALVNIPTLGIVAGLCCAMVLVMGFVGAGASLQLERARKSHPDAA 291

Query: 280 VQNVKILLRLLPIWTMLLMFAVIFQQPVTFFTKQGMAMKRNIGSRFKIPPATLQSAITVS 339
           V  V+ +LR+L ++ ++  F  +F Q  + +  Q   M +     F+  PA +Q+   + 
Sbjct: 292 VDGVRSVLRILVLFALVTPFWSLFDQKASTWILQANDMVKP--QWFE--PAMMQALNPLL 347

Query: 340 IILLMPLYDTVLIPIIQIITCYQFKKGISVMQRMRIGMFLTSIAMVIAAAVETKRLQRSK 399
           ++LL+P  + VL P I+     +    ++ +++M  G+ +T ++ ++   ++      S 
Sbjct: 348 VMLLIPFNNFVLYPAIE-----RMGVKLTALRKMGAGIAITGLSWIVVGTIQLMMDGGSA 402

Query: 400 QAEAKPITIFWLLPEYVLLGISDIFTVVAMQEFFYNEVPVRMRTMGFALYTSVFGVGS 457
                 ++IFW +  Y LL   ++       EF Y++ P  M+    + +T    VG+
Sbjct: 403 ------LSIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMKGTIMSFWTLSVTVGN 454


>pdb|1YIR|A Chain A, Crystal Structure Of A Nicotinate
           Phosphoribosyltransferase
 pdb|1YIR|B Chain B, Crystal Structure Of A Nicotinate
           Phosphoribosyltransferase
 pdb|1YIR|C Chain C, Crystal Structure Of A Nicotinate
           Phosphoribosyltransferase
 pdb|1YIR|D Chain D, Crystal Structure Of A Nicotinate
           Phosphoribosyltransferase
          Length = 408

 Score = 30.8 bits (68), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 11/64 (17%)

Query: 272 NPKNVKHAVQNVKILLRLLPIWTMLLMFAVIFQQPVTFFTKQGMAMKRNIGSRFKIPPAT 331
           NP+ V+  ++N +  LRL   W  +++F V    P+       +AM   + +R + P AT
Sbjct: 98  NPRYVQTGIENDEFFLRLKGPWLHVILFEV----PL-------LAMISEVRNRARYPAAT 146

Query: 332 LQSA 335
           ++ A
Sbjct: 147 VEQA 150


>pdb|3NOY|A Chain A, Crystal Structure Of Ispg (Gcpe)
 pdb|3NOY|B Chain B, Crystal Structure Of Ispg (Gcpe)
 pdb|3NOY|C Chain C, Crystal Structure Of Ispg (Gcpe)
 pdb|3NOY|D Chain D, Crystal Structure Of Ispg (Gcpe)
          Length = 366

 Score = 30.4 bits (67), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 17/82 (20%)

Query: 297 LMFAVIFQQPVTF-FTKQGMAMKRNIGSRFKIPPATLQSAITVSIILLMPLYDTVLI--- 352
           L+FA     P+    T+ GM  K             ++S++ + I+L M + DTV +   
Sbjct: 197 LIFAERTDVPLHIGITEAGMGTK-----------GIIKSSVGIGILLYMGIGDTVRVSLT 245

Query: 353 --PIIQIITCYQFKKGISVMQR 372
             P++++ T Y+  K + + +R
Sbjct: 246 DDPVVEVETAYEILKSLGLRRR 267


  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
   0.324    0.135    0.399 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,811,817
Number of Sequences: 62578
Number of extensions: 351416
Number of successful extensions: 816
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: 812
Number of HSP's gapped (non-prelim): 6
length of query: 478
length of database: 14,973,337
effective HSP length: 103
effective length of query: 375
effective length of database: 8,527,803
effective search space: 3197926125
effective search space used: 3197926125
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)