GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gtsC in Phaeobacter inhibens BS107

Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate GFF774 PGA1_c07880 alpha-glucoside transport system permease protein AglG

Query= TCDB::Q72KX4
         (268 letters)



>lcl|FitnessBrowser__Phaeo:GFF774 PGA1_c07880 alpha-glucoside
           transport system permease protein AglG
          Length = 382

 Score =  135 bits (339), Expect = 2e-36
 Identities = 75/208 (36%), Positives = 112/208 (53%), Gaps = 3/208 (1%)

Query: 63  FQNSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFM 122
           F N++ + + AT++  LV +   Y LA   F G  LL A I+  + +P Q  LIPL +F 
Sbjct: 175 FFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRALLVAAIVGLLVVPLQLALIPLLKFH 234

Query: 123 KSIGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVILP 182
             IG+     G+ + H  +G+P+   + RNY   IP +++E AR+DGA  F IF  +ILP
Sbjct: 235 NEIGIGKGYIGVWMAHTGFGLPLAIYLLRNYMVGIPRDIIENARVDGATDFLIFVRIILP 294

Query: 183 LSVPAFVVVAIWQFTQIWNEFLFAVTL---TRPESQPITVALAQLAGGEAVKWNLPMAGA 239
           LS PA    AI+QF   WN+ L A+        E+  +T  + +L G     W +    A
Sbjct: 295 LSFPALASFAIFQFLWTWNDLLVAMVFLIDATGETTVMTKQIVELLGTRGGNWEILATSA 354

Query: 240 ILAALPTLLVYILLGRYFLRGLLAGSVK 267
            ++    L V+  + +Y +RGLLAGSVK
Sbjct: 355 FVSIAVPLAVFFAMQKYLVRGLLAGSVK 382


Lambda     K      H
   0.330    0.146    0.461 

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: 294
Number of extensions: 13
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: 268
Length of database: 382
Length adjustment: 28
Effective length of query: 240
Effective length of database: 354
Effective search space:    84960
Effective search space used:    84960
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 (21.8 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