GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztB in Escherichia coli BW25113

Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate 1936976 b3269 predicted amino-acid transporter subunit (NCBI)

Query= CharProtDB::CH_011913
         (426 letters)



>FitnessBrowser__Keio:1936976
          Length = 393

 Score =  270 bits (691), Expect = 4e-77
 Identities = 165/405 (40%), Positives = 231/405 (57%), Gaps = 33/405 (8%)

Query: 24  RSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLWTRAGYDLAQTLIPYSNDDT 83
           R+   QI+ ++  +  + WL +N   NL  +G    F+FL   AG+ + Q LI Y   DT
Sbjct: 20  RAWLFQILAVVAVVGIVGWLFHNTVTNLNNRGITSGFAFLDRGAGFGIVQHLIDYQQGDT 79

Query: 84  HFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIPLLLW 143
           + R  I GLLNTLLVS L  + A++LG  IG+ RLS NWL+ ++ T+Y+E FRNIP LL 
Sbjct: 80  YGRVFIVGLLNTLLVSALCIVFASVLGFFIGLARLSDNWLLRKLSTIYIEIFRNIPPLLQ 139

Query: 144 ILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVTNRGTNLPAPAFDHSLG 203
           I      +    P P+     +A+ A           FD   ++NRG  +P+P       
Sbjct: 140 IFFWYFAVLRNLPGPR-----QAVSA-----------FDLAFLSNRGLYIPSP------- 176

Query: 204 VVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTW-WPSLLILFAP 262
              LG      + A+ +  V+S   + +       K  Q  TG    TW   ++LI+  P
Sbjct: 177 --QLGDGFIAFILAVVMAIVLSVGLFRFN------KTYQIKTGQLRRTWPIAAVLIIGLP 228

Query: 263 ISAL-LYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGIQAIS 321
           + A  L+G   H D P +  F+F GG  ++    AL +AL++YT+AFIAEI+RAGIQA+ 
Sbjct: 229 LLAQWLFGAALHWDVPALRGFNFRGGMVLIPELAALTLALSVYTSAFIAEIIRAGIQAVP 288

Query: 322 RGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDLRGTL 381
            GQ EAA +LGL    T+  VI+PQALRVI+PPL SQ+LN+ KNSSLA A+ Y D+    
Sbjct: 289 YGQHEAARSLGLPNPVTLRQVIIPQALRVIIPPLTSQYLNIVKNSSLAAAIGYPDMVSLF 348

Query: 382 GGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLKER 426
            G  LNQTG+ +E + + M +YL ISLTIS LMN+YN+ I + ER
Sbjct: 349 AGTVLNQTGQAIETIAMTMSVYLIISLTISLLMNIYNRRIAIVER 393


Lambda     K      H
   0.326    0.139    0.419 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 391
Number of extensions: 10
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 426
Length of database: 393
Length adjustment: 31
Effective length of query: 395
Effective length of database: 362
Effective search space:   142990
Effective search space used:   142990
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory