Alignments for a candidate for etoh-dh-c in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for etoh-dh-c in Pseudomonas simiae WCS417

Align quinoprotein phenylethanol dehydrogenase; EC 1.1.-.- (characterized)
to candidate GFF3412 PS417_17460 quinonprotein alcohol dehydrogenase

Query= CharProtDB::CH_107431
         (634 letters)



>FitnessBrowser__WCS417:GFF3412
          Length = 615

 Score = 1236 bits (3198), Expect = 0.0
 Identities = 580/619 (93%), Positives = 597/619 (96%), Gaps = 4/619 (0%)

Query: 16  VRVLLLAGGLALGNVATAATAPAAPAAPAGKSVTWEDIANDHLTTKDVLQYGMGTNAQRW 75
           ++  +L G L+L  V  AA  PA P     ++VTWEDIANDHLTT+DVLQYGMGTNAQRW
Sbjct: 1   MQAFVLVGSLSLSAVTFAAAEPAKPT----RTVTWEDIANDHLTTQDVLQYGMGTNAQRW 56

Query: 76  SPLAQVNDQNVFKLTPAWSYSFGDEKQRGQESQAIVSDGVVYVTGSYSRVFALDAKTGKR 135
           SPLAQVND+NVFKLTPAWSYSFGDEKQRGQESQAIVSDGVVYVTGSYSRVFALDAKTGKR
Sbjct: 57  SPLAQVNDKNVFKLTPAWSYSFGDEKQRGQESQAIVSDGVVYVTGSYSRVFALDAKTGKR 116

Query: 136 LWTYNHRLPDNIRPCCDVVNRGAAIFGDKIYFGTLDARLIALDKHTGKVVWNKKFGDHSA 195
           LWTYNHRLPDNIRPCCDVVNRGAAIFGDKIYFGTLDARLIALDK+TGKVVWNKKFGDH+A
Sbjct: 117 LWTYNHRLPDNIRPCCDVVNRGAAIFGDKIYFGTLDARLIALDKNTGKVVWNKKFGDHAA 176

Query: 196 GYTMTGAPVLIKDKTSGKVLLIHGSSGDEFGVVGQLFARDPDTGEEVWMRPFVEGHMGRL 255
           GYT+TGAPVLIKDK SGKVLLIHGSSGDEFGVVGQLFARDPDTGEEVWMRPFVEGHMGRL
Sbjct: 177 GYTLTGAPVLIKDKVSGKVLLIHGSSGDEFGVVGQLFARDPDTGEEVWMRPFVEGHMGRL 236

Query: 256 NGKDSTPTGDVKAPSWPDDPTTETGKVEAWSHGGGAPWQSASFDPETNTIIVGAGNPGPW 315
           NGKDSTPTGDVKAPSWPDDPTTETGKVEAWSHGGGAPWQSASFD ETNTIIVGAGNPGPW
Sbjct: 237 NGKDSTPTGDVKAPSWPDDPTTETGKVEAWSHGGGAPWQSASFDAETNTIIVGAGNPGPW 296

Query: 316 NTWARTSKDGNPHDFDSLYTSGQVGVDPSTGEVKWFYQHTPNDAWDFSGNNELVLFDYKD 375
           NTWART+KDGNPHDFDSLYTSGQVGVDPSTGEVKWFYQHTPNDAWDFSGNNELVLFDYKD
Sbjct: 297 NTWARTAKDGNPHDFDSLYTSGQVGVDPSTGEVKWFYQHTPNDAWDFSGNNELVLFDYKD 356

Query: 376 KNGNVVKATAHADRNGFFYVVDRNNGKLQNAFPFVDNITWASHIDLKTGRPVENPGQRPA 435
           K+G VVKAT HADRNGFFYVVDRNNGKLQNAFPFVDNITWASHIDLKTGRPVEN GQRPA
Sbjct: 357 KDGKVVKATGHADRNGFFYVVDRNNGKLQNAFPFVDNITWASHIDLKTGRPVENEGQRPA 416

Query: 436 KPLPGETKGKPVEVSPPFLGGKNWNPMAYSQDTGLFYIPGNQWKEEYWTEEVNYKKGSAY 495
           KPLPGETKGKPVEVSPPFLGGKNWNPMAYSQDTGLFYIPGNQWKEEYWTEEVNYKKGSAY
Sbjct: 417 KPLPGETKGKPVEVSPPFLGGKNWNPMAYSQDTGLFYIPGNQWKEEYWTEEVNYKKGSAY 476

Query: 496 LGMGFRIKRMYDDHVGTLRAMDPTTGKLVWEHKEHLPLWAGVLATKGNLVFTGTGDGFFK 555
           LGMGFRIKRMYDDHVGTLRAM+PTTGK+VWEHKE LPLWAGVLATKGNLVFTGTGDGFFK
Sbjct: 477 LGMGFRIKRMYDDHVGTLRAMNPTTGKVVWEHKEALPLWAGVLATKGNLVFTGTGDGFFK 536

Query: 556 AFDAKTGKELWKFQTGSGIVSPPITWEQDGEQYIGVTVGYGGAVPLWGGDMAELTKPVAQ 615
           AFDAKTGKELWKFQTGSGIVSPPITWEQDGEQY+GVTVGYGGAVPLWGGDMAELTKPVAQ
Sbjct: 537 AFDAKTGKELWKFQTGSGIVSPPITWEQDGEQYVGVTVGYGGAVPLWGGDMAELTKPVAQ 596

Query: 616 GGSFWVFKIPSWDNKTAQR 634
           GGSFWVFKIPSWDNKTAQ+
Sbjct: 597 GGSFWVFKIPSWDNKTAQK 615


Lambda     K      H
   0.316    0.135    0.435 

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: 2127
Number of extensions: 150
Number of successful extensions: 17
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: 634
Length of database: 615
Length adjustment: 37
Effective length of query: 597
Effective length of database: 578
Effective search space:   345066
Effective search space used:   345066
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 (21.6 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources