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_254914180.1 BZY95_RS08605 iron ABC transporter permease

Query= SwissProt::P15030
         (332 letters)



>NCBI__GCF_002151265.1:WP_254914180.1
          Length = 339

 Score =  178 bits (452), Expect = 1e-49
 Identities = 115/315 (36%), Positives = 179/315 (56%), Gaps = 4/315 (1%)

Query: 17  ALIIIFWLSLFCYSAIPVSGADATRALLPGHTPTLPEALVQNLRLPRSLVAVLIGASLAL 76
           AL+++  L+   + A  V  A A  A+  G      + +V +LRLPR+LV +++G +L +
Sbjct: 24  ALLVLVCLASLLWGAGDVGPARAWAAIT-GQGDAEAQFVVGSLRLPRTLVGLVVGLALGV 82

Query: 77  AGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAGYSLSFIAACGGGVSWLLV 136
           AG LLQ +T NP+A P LLG+++GAA A+A+   L  T  A      +A  G  V  L V
Sbjct: 83  AGALLQAVTRNPLAEPGLLGVSAGAAFAVAVALVLGAT--ATTMRIGVAQLGAMVGCLCV 140

Query: 137 MTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAYGIFYWLAGGVSHARWQD 196
           +         +D  +L+LAG AL+   + LT + LL  +  A  I +W+ G ++  R + 
Sbjct: 141 LGVARVSGAGNDPVRLVLAGAALTGLLLSLTSL-LLFDQRAADEIRFWIVGSLAGRRLEH 199

Query: 197 VWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLLVGACVSV 256
           +  +LP ++ A  +VL +A  L  L+L +  A  LG     +RL++ + V LLVGA  + 
Sbjct: 200 LLAILPSLLLAGAIVLAVARPLAALSLGERVASGLGHRPGLIRLLVIVAVALLVGAATAT 259

Query: 257 AGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFPGDLPAGAVL 316
           AGP+AF+GL+VP  AR  AG D R  L + + LG  +++ AD+++R L  P +LP G + 
Sbjct: 260 AGPIAFVGLVVPFAARALAGPDIRRTLWLCLPLGPLMVITADIVSRLLVAPSELPLGVLT 319

Query: 317 ALIGSPCFVWLVRRR 331
           AL G+P  V +VR R
Sbjct: 320 ALCGAPVLVAVVRAR 334


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: 309
Number of extensions: 11
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: 339
Length adjustment: 28
Effective length of query: 304
Effective length of database: 311
Effective search space:    94544
Effective search space used:    94544
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.

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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