GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF774
          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:

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