GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtB' in Escherichia coli BW25113

Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate 1936976 b3269 predicted amino-acid transporter subunit (NCBI)

Query= uniprot:Q31RP0
         (377 letters)



>FitnessBrowser__Keio:1936976
          Length = 393

 Score =  256 bits (655), Expect = 6e-73
 Identities = 152/368 (41%), Positives = 216/368 (58%), Gaps = 17/368 (4%)

Query: 20  WVWQLL-VLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSAGFNIGESAIAYRTADSY 78
           W++Q+L V+ VVG+   WL  N V NL+ RG++  F +LD+ AGF I +  I Y+  D+Y
Sbjct: 22  WLFQILAVVAVVGIVG-WLFHNTVTNLNNRGITSGFAFLDRGAGFGIVQHLIDYQQGDTY 80

Query: 79  ARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQL 138
            R  +VGL+N+L V A+ ++  +V+G   G+A  S+NWLLR+LS  Y+ + RN P LLQ+
Sbjct: 81  GRVFIVGLLNTLLVSALCIVFASVLGFFIGLARLSDNWLLRKLSTIYIEIFRNIPPLLQI 140

Query: 139 IVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLPWPQT-PGWLVVILAIALVLFVS---- 193
             WYF +L +LP  +Q        +LS +G+Y+P PQ   G++  ILA+ + + +S    
Sbjct: 141 FFWYFAVLRNLPGPRQAVSAFDLAFLSNRGLYIPSPQLGDGFIAFILAVVMAIVLSVGLF 200

Query: 194 ---WLAQRQRSPRDWRWLYGAIAVVTVLMLL-----TQLSWP-QQLQPGQIRGGLRLSLE 244
                 Q +       W   A+ ++ + +L        L W    L+    RGG+ L  E
Sbjct: 201 RFNKTYQIKTGQLRRTWPIAAVLIIGLPLLAQWLFGAALHWDVPALRGFNFRGGMVLIPE 260

Query: 245 FTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALRVIVP 304
             AL L L  YT AFI EIIR GI +VP GQ EAA +LGL    TL Q+++PQALRVI+P
Sbjct: 261 LAALTLALSVYTSAFIAEIIRAGIQAVPYGQHEAARSLGLPNPVTLRQVIIPQALRVIIP 320

Query: 305 SLNSQYVGFAKNSSLAIAVGYPDLYAT-AQTTLNQTGRPVEVFLILMLTYLAINAVISAG 363
            L SQY+   KNSSLA A+GYPD+ +  A T LNQTG+ +E   + M  YL I+  IS  
Sbjct: 321 PLTSQYLNIVKNSSLAAAIGYPDMVSLFAGTVLNQTGQAIETIAMTMSVYLIISLTISLL 380

Query: 364 MNGLQQRL 371
           MN   +R+
Sbjct: 381 MNIYNRRI 388


Lambda     K      H
   0.326    0.140    0.445 

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: 408
Number of extensions: 22
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: 377
Length of database: 393
Length adjustment: 30
Effective length of query: 347
Effective length of database: 363
Effective search space:   125961
Effective search space used:   125961
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