GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aglG' in Marinobacter adhaerens HP15

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate GFF2207 HP15_2161 sugar ABC transporter, permease protein

Query= uniprot:A8LLL4
         (385 letters)



>lcl|FitnessBrowser__Marino:GFF2207 HP15_2161 sugar ABC transporter,
           permease protein
          Length = 269

 Score =  113 bits (283), Expect = 5e-30
 Identities = 71/233 (30%), Positives = 121/233 (51%), Gaps = 9/233 (3%)

Query: 153 PPEFTFANYENMLLDPNNSEGMARAFFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRA 212
           P  FT  NY  +  DP+   G    + N++       +I +LVA  AAYA +  +F G  
Sbjct: 45  PQNFTLDNYAVIFTDPSWYNG----YINSMIYVSINVVITLLVALPAAYAFSRYKFLGDK 100

Query: 213 LLIALIVGLLVVPLQLALIPLLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGL 272
            L   ++   + P  + L+P   L+++IG+   ++   LAH  F +PLA+++L  +M G+
Sbjct: 101 HLFFWLLSNRMAPPAVFLLPFFQLYSSIGLFDTHIAVALAHCLFNVPLAVWILEGFMSGV 160

Query: 273 PRDIIENAKVDGATDFQIFTKIVLPLSFPALASFAIFQFLWTWNDLLVAKVFL-IDATGQ 331
           PR+  E A +DG +  + F K+ LP+    +   A F F+++W +LL+A+    +DA   
Sbjct: 161 PREYDEMAYIDGYSFPKFFVKVFLPMIRSGIGVTAFFAFMFSWVELLLARTLTSVDAQPI 220

Query: 332 TTVMTNQIVELLGTRGGNWEILATAAFVSIAVPLLVFFSMQRFLVRGLLAGSV 384
             +MT  I    G  G +W +LA A  ++I   LLV + ++  + +G   G V
Sbjct: 221 GAIMTRTI----GASGIDWGVLAAAGSLTIIPGLLVIWFVRNHVAKGFALGRV 269


Lambda     K      H
   0.323    0.138    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: 252
Number of extensions: 16
Number of successful extensions: 2
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: 385
Length of database: 269
Length adjustment: 28
Effective length of query: 357
Effective length of database: 241
Effective search space:    86037
Effective search space used:    86037
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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