GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Stenotrophomonas chelatiphaga DSM 21508

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 WP_042615044.1 ABB28_RS00970 carbohydrate ABC transporter permease

Query= TCDB::Q72KX4
         (268 letters)



>NCBI__GCF_001431535.1:WP_042615044.1
          Length = 278

 Score =  151 bits (382), Expect = 1e-41
 Identities = 95/269 (35%), Positives = 151/269 (56%), Gaps = 15/269 (5%)

Query: 8   GFLLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWEAFRP-----K 62
           G LL++A   L P+  +V  ++      T    +  P  P   +F    E F        
Sbjct: 17  GGLLVLALVSLAPLLWMVSVSVMPAGEAT---TFPPPLTPSHVTFANYHELFARTGMGVN 73

Query: 63  FQNSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFM 122
           F NS++++V+ TL S L+ ++ GY  AK  F G   LF +++  + IP Q  ++PLF  M
Sbjct: 74  FANSLLVSVAITLGSLLLNTMAGYAFAKLRFVGRDRLFQVLMAALVIPAQVAMLPLFLLM 133

Query: 123 KSIGLYGSLFGLVL--VHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVI 180
           K +GL  S  G+++  +  ++GI +V    R Y   IPDEL+EAAR+DGAG   IF  ++
Sbjct: 134 KQLGLVNSFGGVIVPALATVFGIFLV----RQYARSIPDELLEAARMDGAGEMRIFFQIV 189

Query: 181 LPLSVPAFVVVAIWQFTQIWNEFLF-AVTLTRPESQPITVALAQLAGGEAVKWNLPMAGA 239
           LP+  P  V ++I+ F   WN+F++  + LT  E   + VALA L+    +   + MAGA
Sbjct: 190 LPMLKPVLVTLSIFTFMGAWNDFMWPLIVLTDQEHYTLPVALATLSREHIMDVEMMMAGA 249

Query: 240 ILAALPTLLVYILLGRYFLRGLLAGSVKG 268
           ++  +P L +++LL RY+++GL+ GSVKG
Sbjct: 250 VVTVIPVLALFLLLQRYYIQGLMLGSVKG 278


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: 216
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: 268
Length of database: 278
Length adjustment: 25
Effective length of query: 243
Effective length of database: 253
Effective search space:    61479
Effective search space used:    61479
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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