BLASTP 2.2.1 [Apr-13-2001]


Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, 
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.

Query= gi|15645507|ref|NP_207682.1| iron(III) dicitrate ABC
transporter, permease protein (fecD) [Helicobacter pylori 26695]
         (326 letters)

Database: /var/www/html/HP/blast_new/blast/db/pdbaa
           13,198 sequences; 2,899,336 total letters

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

pdb|1L7V|A  Chain A, Bacterial Abc Transporter Involved In B...   141  9e-35
pdb|1IWG|A  Chain A, Crystal Structure Of Bacterial Multidru...    28  1.9
pdb|1RYP|L  Chain L, Crystal Structure Of The 20s Proteasome...    26  7.1

>pdb|1L7V|A Chain A, Bacterial Abc Transporter Involved In B12 Uptake
 pdb|1L7V|B Chain B, Bacterial Abc Transporter Involved In B12 Uptake
          Length = 326

 Score =  141 bits (356), Expect = 9e-35
 Identities = 95/282 (33%), Positives = 149/282 (52%), Gaps = 20/282 (7%)

Query: 53  IIILEIRLPRVILALLVGASLSGSGVVMQTIFRNPLVDPFLLGISSGAMLGVAMAIAVVE 112
           + + +IRLPR +  LLVGA+L+ SG V Q +F NPL +P LLG+S+GA +G+  A+ + +
Sbjct: 50  LFVWQIRLPRTLAVLLVGAALAISGAVXQALFENPLAEPGLLGVSNGAGVGLIAAVLLGQ 109

Query: 113 SN-----IAILAFFGAILASLAVLAMNRVLGNSVLSLVLSGVVLSAFLSALAGAIKFFVI 167
                  + + A  GA++ +L +L   R    S   L+L+GV L    SAL     +F  
Sbjct: 110 GQLPNWALGLCAIAGALIITLILLRFAR-RHLSTSRLLLAGVALGIICSALXTWAIYFST 168

Query: 168 PQKAQAIVVWLLGSLSLSSYKDCLIAFIGLSLGFIPLFLLRW------RINLLSLSDAQS 221
               + +  W  G      ++        L L  IP+ L  W        N L+L +  +
Sbjct: 169 SVDLRQLXYWXXGGFGGVDWRQS-----WLXLALIPVLL--WICCQSRPXNXLALGEISA 221

Query: 222 LSLGINPVLLRSLCLVCVSVASALAVSVSGTIGWIGLVIPHVARLFFGANLQKLLLSSLL 281
             LG+     R++ +        ++V+++G IG+IGLVIPH+ RL    + + LL    L
Sbjct: 222 RQLGLPLWFWRNVLVAATGWXVGVSVALAGAIGFIGLVIPHILRLCGLTDHRVLLPGCAL 281

Query: 282 MGAFFLLLADVVAK-TITPYDLPVGIATSVLGAPFFLWLLFR 322
            GA  LLLAD+VA+  +   +LP+G+ T+ LGAP F+WLL +
Sbjct: 282 AGASALLLADIVARLALAAAELPIGVVTATLGAPVFIWLLLK 323



>pdb|1IWG|A Chain A, Crystal Structure Of Bacterial Multidrug Efflux
           Transporter Acrb
          Length = 1053

 Score = 27.7 bits (60), Expect = 1.9
 Identities = 17/70 (24%), Positives = 38/70 (54%), Gaps = 7/70 (10%)

Query: 94  LGISSGAMLGVAMAIAVVESNIAILAFF----GAILASLAVLAMNRVLGNSVLSLVLSGV 149
           +G   GA++G+AM ++ V      +AFF    GAI    ++  ++ +  + +++L+L+  
Sbjct: 435 MGQIQGALVGIAMVLSAV---FVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPA 491

Query: 150 VLSAFLSALA 159
           + +  L  +A
Sbjct: 492 LCATMLKPIA 501



>pdb|1RYP|L Chain L, Crystal Structure Of The 20s Proteasome From Yeast At
          2.4 Angstroms Resolution
 pdb|1RYP|Z Chain Z, Crystal Structure Of The 20s Proteasome From Yeast At
          2.4 Angstroms Resolution
 pdb|1FNT|L Chain L, Crystal Structure Of The 20s Proteasome From Yeast In
          Complex With The Proteasome Activator Pa26 From
          Trypanosome Brucei At 3.2 Angstroms Resolution
 pdb|1FNT|Z Chain Z, Crystal Structure Of The 20s Proteasome From Yeast In
          Complex With The Proteasome Activator Pa26 From
          Trypanosome Brucei At 3.2 Angstroms Resolution
          Length = 212

 Score = 25.8 bits (55), Expect = 7.1
 Identities = 14/44 (31%), Positives = 23/44 (51%)

Query: 56 LEIRLPRVILALLVGASLSGSGVVMQTIFRNPLVDPFLLGISSG 99
          L  R    I+  +   + +G+ V  QT+ R   ++PFLLG  +G
Sbjct: 4  LAFRFQGGIIVAVDSRATAGNWVASQTVKRVIEINPFLLGTMAG 47



  Database: /var/www/html/HP/blast_new/blast/db/pdbaa
    Posted date:  Dec 20, 2002 11:08 AM
  Number of letters in database: 2,899,336
  Number of sequences in database:  13,198
  
Lambda     K      H
   0.329    0.143    0.413 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,513,012
Number of Sequences: 13198
Number of extensions: 49596
Number of successful extensions: 142
Number of sequences better than 10.0: 3
Number of HSP's better than 10.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 137
Number of HSP's gapped (non-prelim): 3
length of query: 326
length of database: 2,899,336
effective HSP length: 88
effective length of query: 238
effective length of database: 1,737,912
effective search space: 413623056
effective search space used: 413623056
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 54 (25.4 bits)