GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lldE in Shewanella oneidensis MR-1

Align L-lactate dehydrogenase complex protein LldE (characterized, see rationale)
to candidate 200691 SO1520 conserved hypothetical protein (NCBI ptt file)

Query= uniprot:Q8EGS4
         (247 letters)



>FitnessBrowser__MR1:200691
          Length = 247

 Score =  500 bits (1287), Expect = e-146
 Identities = 247/247 (100%), Positives = 247/247 (100%)

Query: 1   MKIALFIPCLVNQMMPDVAIATLELLEKLGHQVILPAGQTCCGQPMTNSGCFDAARSTTL 60
           MKIALFIPCLVNQMMPDVAIATLELLEKLGHQVILPAGQTCCGQPMTNSGCFDAARSTTL
Sbjct: 1   MKIALFIPCLVNQMMPDVAIATLELLEKLGHQVILPAGQTCCGQPMTNSGCFDAARSTTL 60

Query: 61  KLLNAFKGVECDAIVCPAASCLVAAKENFHEFDNSPEAQAVINKLYELTEFLHDIAPIPA 120
           KLLNAFKGVECDAIVCPAASCLVAAKENFHEFDNSPEAQAVINKLYELTEFLHDIAPIPA
Sbjct: 61  KLLNAFKGVECDAIVCPAASCLVAAKENFHEFDNSPEAQAVINKLYELTEFLHDIAPIPA 120

Query: 121 FNKPFAHKISLQLSCHGIRMLSLATPSEQMGPRFNKVEAVLANIAGIDIVYPDRRDECCG 180
           FNKPFAHKISLQLSCHGIRMLSLATPSEQMGPRFNKVEAVLANIAGIDIVYPDRRDECCG
Sbjct: 121 FNKPFAHKISLQLSCHGIRMLSLATPSEQMGPRFNKVEAVLANIAGIDIVYPDRRDECCG 180

Query: 181 FGGTFAVDEGAVSAKMGKDKAQAHAATGAQYVVGFDPSCLLHLDGLIRRQQLPIEIRHIA 240
           FGGTFAVDEGAVSAKMGKDKAQAHAATGAQYVVGFDPSCLLHLDGLIRRQQLPIEIRHIA
Sbjct: 181 FGGTFAVDEGAVSAKMGKDKAQAHAATGAQYVVGFDPSCLLHLDGLIRRQQLPIEIRHIA 240

Query: 241 QVLNAAL 247
           QVLNAAL
Sbjct: 241 QVLNAAL 247


Lambda     K      H
   0.324    0.137    0.416 

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: 355
Number of extensions: 5
Number of successful extensions: 1
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: 247
Length of database: 247
Length adjustment: 24
Effective length of query: 223
Effective length of database: 223
Effective search space:    49729
Effective search space used:    49729
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 46 (22.3 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