GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucO in Williamsia sterculiae CPCC 203464

Align NADH-dependent aldehyde reductase (EC 1.1.1.77; EC 1.1.1.244; EC 1.1.1.1) (characterized)
to candidate WP_076477985.1 BW971_RS07365 SDR family oxidoreductase

Query= metacyc::G3O-32155-MONOMER
         (298 letters)



>NCBI__GCF_900156495.1:WP_076477985.1
          Length = 293

 Score =  189 bits (480), Expect = 7e-53
 Identities = 114/295 (38%), Positives = 166/295 (56%), Gaps = 11/295 (3%)

Query: 1   MKVFITGASGFIGSAVLSELISSGHEVVGLARSDEAAAKIKSIDPAAKILRGDLKDLEIL 60
           M VF+TG +G IGSAV+ EL+++ H V+ LARSD +A  +      A+++RG + DL+ L
Sbjct: 1   MHVFVTGGTGTIGSAVVDELLANDHTVLALARSDASADALARA--GAEVVRGTIADLDTL 58

Query: 61  KKGATESDGVIHLGFVHDFKNFE--QCCEIDRQATVAML-ESLKGSNKPFLYTNGTLSLR 117
              A  +DGVI L F  D+   +      ++  A +A L E+L GS +P +  +GT  + 
Sbjct: 59  STSAGRADGVISLAFTPDYDTPDGLAAAVVEEGAALASLGEALLGSGRPIVTVSGTPWI- 117

Query: 118 PNKVANEQDGIDEDSKIL-RAVTEQVALSYKDKGVSARIVRLPFSVHGKGDKAFVPILMN 176
           P +++ E+D + E+  +  RAV+    L    +GV A  VR+P +VH +G   F  +L  
Sbjct: 118 PGRLSTERDPLPEEGPVGGRAVSVNRLLELSSRGVRAVAVRMPRTVHNRGTGGFAGLLTE 177

Query: 177 IAKAAGKSGYVGQGTNAWAAVHRLDTAPLFRLVLEKGKTGQVYHCVGEQGIPFKDIARVI 236
            A+  G +GY G G   W AVH LD A LFRL LE    G  +H V ++G   +DIA VI
Sbjct: 178 QARRTGVAGYPGDGAQRWPAVHALDAAVLFRLALESAPAGTAWHAVADEGDAVRDIASVI 237

Query: 237 GEILNVPVASIPVDDAESHFGFLTCFVTRDGPVSSEGTRKELGWQPQQIGLLEDI 291
           G  L++PV S+    +E   G        D P SS  TR+ LGW+P  +GLLED+
Sbjct: 238 GRRLDLPVESV----SEQSLGPFGPVFALDQPASSAHTRETLGWEPVHLGLLEDL 288


Lambda     K      H
   0.318    0.136    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: 229
Number of extensions: 7
Number of successful extensions: 4
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: 298
Length of database: 293
Length adjustment: 26
Effective length of query: 272
Effective length of database: 267
Effective search space:    72624
Effective search space used:    72624
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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