GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecC in Shewanella loihica PV-4

Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate 5208201 Shew_0713 transport system permease protein (RefSeq)

Query= SwissProt::P15030
         (332 letters)



>FitnessBrowser__PV4:5208201
          Length = 347

 Score =  156 bits (395), Expect = 6e-43
 Identities = 98/274 (35%), Positives = 150/274 (54%), Gaps = 7/274 (2%)

Query: 59  LRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPT---P 115
           LRLPR L+A + G  LALAG +LQT+T NP+A P L GI+SGA+L   +   L       
Sbjct: 71  LRLPRILLAFIAGFGLALAGAVLQTVTRNPLADPYLFGISSGASLGAVVVITLLGGVGGA 130

Query: 116 IAGYSLSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLA- 174
           +A   L   A  G  ++ L+V+   G   +T    +++L+G+A+S     L  + L  + 
Sbjct: 131 LASVGLPLGAFIGASLAVLMVLALCGRDLNTQIE-RMLLSGVAISFLFGALASLMLYFSG 189

Query: 175 EDHAYGIFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVN 234
              A  + +W  G  + A WQ +W    +V+ A  ++LLL  Q+  +   D TAHTLG+ 
Sbjct: 190 PQSAASVLFWSLGSFAKASWQMLWLPWLLVLAASAILLLLKRQILAIQAGDETAHTLGIR 249

Query: 235 LTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLM 294
           + RLRLV  +L  L+    V+  G + F+GL+VPH+ R       R  L ++ L+G   M
Sbjct: 250 VQRLRLVSLLLCSLITAVLVANCGGIGFVGLMVPHMVRLL--LPGRFALLLTALVGGLFM 307

Query: 295 LLADVLARALAFPGDLPAGAVLALIGSPCFVWLV 328
           +  DVLAR L    +LP G + A+IGS  F++++
Sbjct: 308 IWVDVLARCLLSYQELPVGIITAVIGSLFFLFIL 341


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: 354
Number of extensions: 21
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: 332
Length of database: 347
Length adjustment: 28
Effective length of query: 304
Effective length of database: 319
Effective search space:    96976
Effective search space used:    96976
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 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