GapMind for catabolism of small carbon sources

 

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

Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate 5208200 Shew_0712 ABC transporter-related protein (RefSeq)

Query= CharProtDB::CH_088321
         (255 letters)



>FitnessBrowser__PV4:5208200
          Length = 324

 Score =  170 bits (430), Expect = 4e-47
 Identities = 92/248 (37%), Positives = 141/248 (56%), Gaps = 3/248 (1%)

Query: 3   LRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLG 62
           L   +L+   G   +L+ V L LP GK+  +IGPNG GKS+LL C  R L P SG + L 
Sbjct: 36  LSVRDLSWRCGERAILSGVKLDLPEGKMLGIIGPNGAGKSSLLRCLYRFLTPSSGEIQLF 95

Query: 63  DNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNVA 122
             PI  LS+R  AR ++++ Q       +T  +LV+ G  P  + +   +  D   V+ A
Sbjct: 96  GQPIASLSARAFAREVAVVLQDTPQHFDMTTAQLVALGLTPHKAAFSMTTKADRLAVSQA 155

Query: 123 MNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRLMG 182
           +    +   A +    LSGG++QRA +A  +AQ   +++LDEPT +LDI +Q+ ++ L  
Sbjct: 156 LETVGLKERAGQTYASLSGGEKQRALIARAIAQQPKLLILDEPTNHLDIRYQIQILEL-- 213

Query: 183 ELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEAEIH 242
            L+  G TVV  +HDLN AS  CDQL+++  G  +AQG+P++V++   +  VF V  ++ 
Sbjct: 214 -LKALGVTVVISIHDLNLASALCDQLLLLDQGKAVAQGSPKQVLSEAQIARVFCVCCQVS 272

Query: 243 PEPVSGRP 250
           P P  G P
Sbjct: 273 PHPQHGNP 280


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: 199
Number of extensions: 6
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: 255
Length of database: 324
Length adjustment: 26
Effective length of query: 229
Effective length of database: 298
Effective search space:    68242
Effective search space used:    68242
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: 47 (22.7 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