GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecE in Dyella japonica UNC79MFTsu3.2

Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein

Query= CharProtDB::CH_088321
         (255 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1562
          Length = 384

 Score =  108 bits (271), Expect = 1e-28
 Identities = 76/226 (33%), Positives = 114/226 (50%), Gaps = 3/226 (1%)

Query: 1   MTLRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVF 60
           M+L    LT  YG    L+D SL +  G+  AL+GP+G GKS+LL   + L  P  G V 
Sbjct: 1   MSLSIRQLTRRYGAFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVL 60

Query: 61  LGDNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVN 120
                +  L +++  R + L+ QH+     +TV + +++G             +  ARV 
Sbjct: 61  RDGTDLLALPAQR--RDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVE 118

Query: 121 VAMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRL 180
             + + ++  L  R  T+LSGGQRQR  LA  LA    ++LLDEP   LD   +  L   
Sbjct: 119 DLLRRVQLEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVW 178

Query: 181 MGEL-RTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEV 225
           + +L R+ G T V V HD ++A    D++VVM  G +   G P E+
Sbjct: 179 LRDLQRSLGLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEI 224


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: 212
Number of extensions: 16
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: 384
Length adjustment: 27
Effective length of query: 228
Effective length of database: 357
Effective search space:    81396
Effective search space used:    81396
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 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