GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Sphingopyxis indica DS15

Align Alcohol dehydrogenase class-3; EC 1.1.1.1; Alcohol dehydrogenase class-III; Glutathione-dependent formaldehyde dehydrogenase; FALDH; FDH; GSH-FDH; EC 1.1.1.-; S-(hydroxymethyl)glutathione dehydrogenase; EC 1.1.1.284 (uncharacterized)
to candidate WP_089216373.1 CHB69_RS12640 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase

Query= curated2:P72324
         (376 letters)



>NCBI__GCF_900188185.1:WP_089216373.1
          Length = 370

 Score =  581 bits (1498), Expect = e-170
 Identities = 286/377 (75%), Positives = 322/377 (85%), Gaps = 8/377 (2%)

Query: 1   MRTRAAVAVEAGKPLEIMEVNLEGPKAGEVMVEIKATGICHTDEFTLSGADPEGMFPAIL 60
           M+TRAAVA EA KPLEI+E++LEGPKAGEV+VEI ATGICHTD +TL G D EG+FP++L
Sbjct: 1   MKTRAAVAFEAKKPLEIVELDLEGPKAGEVLVEIMATGICHTDAYTLGGFDSEGIFPSVL 60

Query: 61  GHEGAGVVVEVGPGVTSVKPGDHVIPLYTPECRQCPSCLSQKTNLCTAIRGTQGQGLMPD 120
           GHEGAGVV EVG GVTSV PGDHVIPLYTPECRQC SCLS KTNLCTAIR TQG+GLMPD
Sbjct: 61  GHEGAGVVREVGAGVTSVVPGDHVIPLYTPECRQCKSCLSGKTNLCTAIRATQGKGLMPD 120

Query: 121 GTSRFSMLDGTPILHYMGCSTFSNYTVLPEIAVAKVRPDAPFDKICYIGCGVTTGIGAVI 180
           GT+RFS   G PI HYMGCSTFSN+TVLPEIAVAK+R DAPF   CYIGCGVTTG+GAVI
Sbjct: 121 GTTRFS-YKGQPIFHYMGCSTFSNFTVLPEIAVAKIREDAPFQSSCYIGCGVTTGVGAVI 179

Query: 181 NTAKVEIGAKAVVFGLGGIGLNVIQGLKLAGADMIIGVDLNNAKKEWGERFGMTHFVNPS 240
           NTAKV++G   VVFGLGGIGLNVIQG +LAGA+ IIGVD+N A++EWG +FGMT F+N  
Sbjct: 180 NTAKVQVGDNVVVFGLGGIGLNVIQGARLAGANKIIGVDINPAREEWGRKFGMTEFLNSK 239

Query: 241 EID-GDVVAHLVNMTKTPFDQIGGADYTFDCTGNVKVMRQALEACHRGWGQSIVIGVAPA 299
            +   DVVA +V MT       GGADYTFD TGN +VMR ALEACHRGWG SI+IGVA A
Sbjct: 240 GMSREDVVAAIVRMTD------GGADYTFDATGNTEVMRTALEACHRGWGTSIIIGVAEA 293

Query: 300 GAEIQTRPFQLVTGRVWKGSAFGGARGRTDVPKIVDWYMEGKIQIDPMITHILSLEEINK 359
           G EI TRPFQLVTGR W+G+AFGGA+GRTDVPKIVD YM+GKI+IDPMITH++ LE+INK
Sbjct: 294 GKEIATRPFQLVTGRNWRGTAFGGAKGRTDVPKIVDMYMQGKIEIDPMITHVMGLEDINK 353

Query: 360 GFDLMHAGESIRSVVVF 376
           GFDLMHAGESIRSVVV+
Sbjct: 354 GFDLMHAGESIRSVVVY 370


Lambda     K      H
   0.320    0.139    0.427 

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: 566
Number of extensions: 18
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: 376
Length of database: 370
Length adjustment: 30
Effective length of query: 346
Effective length of database: 340
Effective search space:   117640
Effective search space used:   117640
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: 50 (23.9 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