GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecC in Halomonas desiderata SP1

Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate WP_086511917.1 BZY95_RS21415 iron ABC transporter permease

Query= SwissProt::P15030
         (332 letters)



>NCBI__GCF_002151265.1:WP_086511917.1
          Length = 352

 Score =  176 bits (447), Expect = 6e-49
 Identities = 116/321 (36%), Positives = 173/321 (53%), Gaps = 4/321 (1%)

Query: 15  VAALIIIFWLSLFCYSAIPVSGADATRALLPGHTPTLPEALVQNLRLPRSLVAVLIGASL 74
           V AL+ +  L     +A+  S   + R LL      L   +   LRLPR ++A L+GA L
Sbjct: 28  VLALLALAVLVALLAAAMSGSVGLSPRVLLGEWPSPLAWQVWWQLRLPRLILAALVGAML 87

Query: 75  ALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAGYSL--SFIAACGGGVS 132
           A +G  +Q L  NP+A P+LLG+ SGA LA+AL   L         L   F+A   G + 
Sbjct: 88  AGSGAAMQGLFRNPLADPTLLGLASGAGLAVALWIVLLDGAAGSLGLYGQFLAGFLGALG 147

Query: 133 WLLVMTAGGGFRHTHDRN-KLILAGIALSAFCMGLTRITLLLAEDHAYG-IFYWLAGGVS 190
             +++ A G  +H  +    L+LAG+A++     +  +   +A D     +  W  G +S
Sbjct: 148 VCVLVFALGQRQHGQEALFTLLLAGLAINTLAGAMGGVMAFIASDEQLRQLSLWGMGSLS 207

Query: 191 HARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLLV 250
           HA W      L  +  A+  +L  A  L+LL L + TAH  G++  RL+  + +   L V
Sbjct: 208 HALWSATLGALVGIPPALWWLLRCARGLDLLQLGELTAHGAGLDAPRLKRHVVVATALGV 267

Query: 251 GACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFPGDL 310
           G CV++AG + F+GLLVPH  R W G   R +LP SML GA L+++AD LAR LA P ++
Sbjct: 268 GLCVALAGIIGFLGLLVPHCLRLWLGPGHRLLLPASMLGGALLLIVADTLARTLASPAEV 327

Query: 311 PAGAVLALIGSPCFVWLVRRR 331
           P G + +L+G P F+WL+ +R
Sbjct: 328 PVGLLTSLLGGPYFLWLLLKR 348


Lambda     K      H
   0.327    0.140    0.436 

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: 400
Number of extensions: 26
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: 332
Length of database: 352
Length adjustment: 29
Effective length of query: 303
Effective length of database: 323
Effective search space:    97869
Effective search space used:    97869
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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