GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Jannaschia aquimarina GSW-M26

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_043919940.1 jaqu_RS15645 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase

Query= curated2:P72324
         (376 letters)



>NCBI__GCF_000877395.1:WP_043919940.1
          Length = 370

 Score =  633 bits (1633), Expect = 0.0
 Identities = 305/376 (81%), Positives = 340/376 (90%), Gaps = 6/376 (1%)

Query: 1   MRTRAAVAVEAGKPLEIMEVNLEGPKAGEVMVEIKATGICHTDEFTLSGADPEGMFPAIL 60
           MRTRAAVA+EAGKPLE+M+V L+GPKAGEVMVEIKATGICHTDEFTLSGADPEG+FPAIL
Sbjct: 1   MRTRAAVALEAGKPLEVMDVELDGPKAGEVMVEIKATGICHTDEFTLSGADPEGLFPAIL 60

Query: 61  GHEGAGVVVEVGPGVTSVKPGDHVIPLYTPECRQCPSCLSQKTNLCTAIRGTQGQGLMPD 120
           GHEGAGVVVEVG GVTS++ GDHVIPLYTPECR+C  CL+ KTNLC AIR TQGQG+MPD
Sbjct: 61  GHEGAGVVVEVGEGVTSLEVGDHVIPLYTPECRECDYCLNPKTNLCQAIRSTQGQGVMPD 120

Query: 121 GTSRFSMLDGTPILHYMGCSTFSNYTVLPEIAVAKVRPDAPFDKICYIGCGVTTGIGAVI 180
           GTSRF M DGTPILHYMGCSTF+N+TV+PEIA+AKVR DAPF+KICYIGCGVTTGIGAVI
Sbjct: 121 GTSRFRMTDGTPILHYMGCSTFANHTVMPEIALAKVRRDAPFEKICYIGCGVTTGIGAVI 180

Query: 181 NTAKVEIGAKAVVFGLGGIGLNVIQGLKLAGADMIIGVDLNNAKKEWGERFGMTHFVNPS 240
           NTAKVEIG++AVVFGLGGIGLNVIQGL+LAGAD I+GVDLN  K+   ERFGMT FVNP 
Sbjct: 181 NTAKVEIGSRAVVFGLGGIGLNVIQGLRLAGADQIVGVDLNPDKRAMAERFGMTDFVNPG 240

Query: 241 EIDGDVVAHLVNMTKTPFDQIGGADYTFDCTGNVKVMRQALEACHRGWGQSIVIGVAPAG 300
           ++ GD+VAHLV +T       GGADYTFD TGNV VMR ALEA H+GWG+S++IGVAPAG
Sbjct: 241 DVSGDMVAHLVELTG------GGADYTFDATGNVDVMRTALEAAHKGWGESVIIGVAPAG 294

Query: 301 AEIQTRPFQLVTGRVWKGSAFGGARGRTDVPKIVDWYMEGKIQIDPMITHILSLEEINKG 360
           AEI TRPFQLVTGRVW+G+AFGGARGRTDVP+IVDWYM+GKI+IDPMITH LSLE IN+G
Sbjct: 295 AEIATRPFQLVTGRVWRGTAFGGARGRTDVPRIVDWYMDGKIEIDPMITHTLSLENINEG 354

Query: 361 FDLMHAGESIRSVVVF 376
           FDLMH GESIRSVVV+
Sbjct: 355 FDLMHRGESIRSVVVY 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: 620
Number of extensions: 16
Number of successful extensions: 2
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