GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fdh in Marinobacter adhaerens HP15

Align Short-chain dehydrogenase (characterized, see rationale)
to candidate GFF901 HP15_880 oxidoreductase, short chain dehydrogenase/reductase family

Query= uniprot:A0A2E7P8M8
         (258 letters)



>lcl|FitnessBrowser__Marino:GFF901 HP15_880 oxidoreductase, short
           chain dehydrogenase/reductase family
          Length = 243

 Score = 98.6 bits (244), Expect = 1e-25
 Identities = 82/242 (33%), Positives = 123/242 (50%), Gaps = 12/242 (4%)

Query: 12  VTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAALFQL-ELQDEARC 70
           +TGGA GIG  I L LAA G   V F   + D     RL      A  F   ++  E   
Sbjct: 1   MTGGAKGIGRGIVLHLAAAGW-KVAFC--DTDSAVGERLAAGADYALHFLPGDVASETDV 57

Query: 71  GEAVAETVRRFGRLDGLVNNAGV-NDSVGL--DAGRNEFVASLERNLIHYYVMAHYCVPH 127
              VAE +R  GRLD ++NNAG+ N   G   +   +++   L+ NL   +++  + VPH
Sbjct: 58  ERIVAEALRWGGRLDAVINNAGIANPETGPIEELSLDQWQRRLDVNLTGPFLVTKHAVPH 117

Query: 128 LKATRGAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRVNALIPAEVM 187
           L+ T+GAI+N++S  AL  + +T  Y A+KG  ++LT   A +L  D VRVN + P  + 
Sbjct: 118 LRKTKGAIVNMASTRALQSEPDTEAYAATKGGIVALTHALAVSLGPD-VRVNCISPGWID 176

Query: 188 TPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRSSHTTGQWVFVD 247
           T  ++      E P  + D +  + P G R     ++A +  +L+S  +S  TGQ    D
Sbjct: 177 TRAWQGGAEPVE-PLSENDHL--QHPAG-RVGQPGDIASLVAYLISQEASFITGQNFVAD 232

Query: 248 GG 249
           GG
Sbjct: 233 GG 234


Lambda     K      H
   0.318    0.134    0.394 

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: 159
Number of extensions: 8
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: 258
Length of database: 243
Length adjustment: 24
Effective length of query: 234
Effective length of database: 219
Effective search space:    51246
Effective search space used:    51246
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 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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