GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecE in Thiothrix lacustris DSM 21227

Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein

Query= CharProtDB::CH_088321
         (255 letters)



>NCBI__GCF_000621325.1:WP_028489030.1
          Length = 348

 Score = 94.4 bits (233), Expect = 3e-24
 Identities = 74/240 (30%), Positives = 116/240 (48%), Gaps = 21/240 (8%)

Query: 3   LRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLG 62
           L  +N+   YG    +  VSL + +G+    +GP+GCGKSTLL   + L +   G + L 
Sbjct: 4   LELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQLILD 63

Query: 63  DNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNA----R 118
              I  +   Q  R L+++ Q +     +TV+E +S+          RL+  D A    +
Sbjct: 64  GRDITEVPPSQ--RDLAMVFQSYALYPHMTVEENMSFAL--------RLAKVDPAIIQEK 113

Query: 119 VNVAMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDI----NHQ 174
           V +A ++  +     R    LSGGQRQR  +   + ++  V L DEP + LD     N +
Sbjct: 114 VKMAADKLNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTR 173

Query: 175 VDLMRLMGELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTV 234
           V++  L  EL   G T V V HD  +A    D++VV+ +G +   GTP E+    + R V
Sbjct: 174 VEIASLHREL---GATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFV 230


Lambda     K      H
   0.320    0.134    0.393 

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: 197
Number of extensions: 9
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: 255
Length of database: 348
Length adjustment: 26
Effective length of query: 229
Effective length of database: 322
Effective search space:    73738
Effective search space used:    73738
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 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