GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecC in Marinobacter adhaerens HP15

Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate GFF3640 HP15_3582 transport system permease protein

Query= SwissProt::P15030
         (332 letters)



>FitnessBrowser__Marino:GFF3640
          Length = 326

 Score =  169 bits (428), Expect = 9e-47
 Identities = 102/313 (32%), Positives = 173/313 (55%), Gaps = 10/313 (3%)

Query: 24  LSLFCYSAIPVSGADATR----ALLPGHTPTLPEALVQNLRLPRSLVAVLIGASLALAGT 79
           L+L  + A+ +   + T     A L G   T  + +V N+RLPR   A+L+GA+LA AG 
Sbjct: 12  LTLLAFGAVMIGPYNLTPGQTLAALLGQGDTQAQIVVWNIRLPRVAAALLVGAALAAAGA 71

Query: 80  LLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAGYSLSFIAACGGGVSWLLVMTA 139
             Q L  NP+ SP +LG+++GA L  A+       P+A    S  A  GG ++   V+  
Sbjct: 72  SYQALFRNPLVSPDILGVSAGAGLG-AVAGIFLSLPVAAIQAS--AFVGGMLAVGFVILV 128

Query: 140 GGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAE--DHAYGIFYWLAGGVSHARWQDV 197
               R+T     L+L G+ + A     T +  ++A+  D    I +WL G ++    +D+
Sbjct: 129 ASLVRNTDRTLTLVLIGVVIGALAGAATSLLKVMADPYDQLPAITFWLLGSLAATTTEDI 188

Query: 198 WQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLLVGACVSVA 257
              LP+V+  +  + LL  ++N+L+L D  A  LG+++++ R ++ +   L+  +  ++A
Sbjct: 189 LPTLPMVLIGLVPLALLRWRINVLSLGDEEARALGIDVSKTRFLVIVAATLITASVTALA 248

Query: 258 GPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFPGDLPAGAVLA 317
           G V ++GL++PH+AR   G     +LP S+L+GA  +L+ D LAR +A   ++P G + A
Sbjct: 249 GVVGWVGLVIPHIARMLVGPGFGRLLPTSVLIGAGYLLVVDTLARTMA-QVEVPLGILTA 307

Query: 318 LIGSPCFVWLVRR 330
           +IG+P FVWL+ R
Sbjct: 308 VIGAPFFVWLLAR 320


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: 332
Number of extensions: 21
Number of successful extensions: 4
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: 326
Length adjustment: 28
Effective length of query: 304
Effective length of database: 298
Effective search space:    90592
Effective search space used:    90592
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