GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecD in Corynebacterium lactis RW2-5

Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate WP_053412606.1 CLAC_RS08855 iron ABC transporter permease

Query= CharProtDB::CH_004160
         (318 letters)



>NCBI__GCF_001274895.1:WP_053412606.1
          Length = 327

 Score =  196 bits (499), Expect = 5e-55
 Identities = 115/319 (36%), Positives = 180/319 (56%), Gaps = 6/319 (1%)

Query: 2   KIALVIFITLA-LAGCALLSLHMGVIPVPWRALLTDWQAGHEHYYVLMEYRLPRLLLALF 60
           + ALV+ ++ A L    LL + +G +      +++   AG   Y+    YR+PR+++ + 
Sbjct: 6   RFALVLVVSTAFLVLACLLGMGIGAVQKSLPDVISGLLAGENLYW---RYRMPRIVVGVL 62

Query: 61  VGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVLPLLAFAGGM 120
            G  +AVAG L+Q  +RNPLA+PD LG+     LA+V ALL   SLP + L  +AF G +
Sbjct: 63  AGVGMAVAGSLLQTALRNPLAAPDTLGITAGGGLAAVVALLGFGSLPPLALTPIAFVGSL 122

Query: 121 AGLILLKMLA--KTHQPMKLALTGVALSACWASLTDYLMLSRPQDVNNALLWLTGSLWGR 178
            G + +   A      P +LALTGVA+S   A++T  L++    +   A+ WL GSL+ R
Sbjct: 123 LGALAVFATAGRAVADPARLALTGVAVSVGLAAVTQLLLVRVAPEAGAAMTWLKGSLYAR 182

Query: 179 DWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALLLAVAMTST 238
             S      P+++    ++++  R  + L L D+   ++GV     R  AL++AVA  S 
Sbjct: 183 TMSDALTVAPVVVAGAVVAMAVARHFNTLVLDDSTMASIGVRSNVLRILALIIAVACGSA 242

Query: 239 GVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARIIHPPLELPV 298
            VAA G + F+GL++PH  + + G    R +PV A+ GA L+V AD + R    P E+PV
Sbjct: 243 AVAAAGVLGFVGLIIPHAAKLLVGQNLARQIPVGAVAGAALVVAADAVGRWAFAPTEIPV 302

Query: 299 GVLTAIIGAPWFVWLLVRM 317
           G L AI GAP+F++L+ R+
Sbjct: 303 GALIAIAGAPYFIYLVHRV 321


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: 245
Number of extensions: 9
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: 327
Length adjustment: 28
Effective length of query: 290
Effective length of database: 299
Effective search space:    86710
Effective search space used:    86710
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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