GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecD in Nocardiopsis lucentensis DSM 44048

Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate WP_017601334.1 D471_RS0126060 iron chelate uptake ABC transporter family permease subunit

Query= CharProtDB::CH_004160
         (318 letters)



>NCBI__GCF_000341125.1:WP_017601334.1
          Length = 366

 Score =  196 bits (499), Expect = 5e-55
 Identities = 119/318 (37%), Positives = 171/318 (53%), Gaps = 6/318 (1%)

Query: 5   LVIFITLALAGCALLSLHMGVIPVPWRALLTDWQAGHEHYYVLMEYRLPRLLLALFVGAA 64
           L + + LA     L    M      W+AL     A  E   ++ E RLPR  L L  G +
Sbjct: 47  LAVLLGLAALSSVLFGARMLDPATVWQAL--SHAASDEANIIVNEIRLPRTALGLLAGLS 104

Query: 65  LAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVLPLLAFAGGMAGLI 124
           L + G L+QG  RNPL  P ILGV   A+   V  +  +    +     LAF G  A  +
Sbjct: 105 LGLGGALMQGHTRNPLGDPSILGVTFGAAFVVVLGIHFLAIDDLRTQAWLAFVGAGAAAV 164

Query: 125 LLKMLAKTH----QPMKLALTGVALSACWASLTDYLMLSRPQDVNNALLWLTGSLWGRDW 180
           ++ ++         P+ LAL G A+S    SL   ++L     ++N   W  GSL GRD 
Sbjct: 165 VVYLIGSVPGRGPTPITLALAGTAVSWLMYSLVSGIVLLDQDTMDNFRFWRVGSLTGRDP 224

Query: 181 SFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALLLAVAMTSTGV 240
           S +   +P +++ + L+L+  R L+ LALGD  A  LG  +   R   LL    +T   V
Sbjct: 225 SVIGQMLPFVVVGVVLALANTRALNALALGDDTARALGFRIGWARATGLLAITLLTGVTV 284

Query: 241 AACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARIIHPPLELPVGV 300
           AACGPI+F+GL+VPH+ R++ G  HR LLP S L GA+LL+ AD+L R + PP EL VGV
Sbjct: 285 AACGPIAFVGLIVPHLARAMVGSDHRWLLPYSGLLGAILLMAADVLGRFLAPPGELQVGV 344

Query: 301 LTAIIGAPWFVWLLVRMR 318
           + AI+GAP+F++++ R +
Sbjct: 345 VLAILGAPFFIYVVRRRK 362


Lambda     K      H
   0.330    0.142    0.447 

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: 287
Number of extensions: 8
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: 318
Length of database: 366
Length adjustment: 29
Effective length of query: 289
Effective length of database: 337
Effective search space:    97393
Effective search space used:    97393
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: 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