Alignments for a candidate for etoh-dh-c in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for etoh-dh-c in Pseudomonas fluorescens FW300-N2C3

Align quinoprotein phenylethanol dehydrogenase; EC 1.1.-.- (characterized)
to candidate AO356_28055 AO356_28055 quinonprotein alcohol dehydrogenase

Query= CharProtDB::CH_107431
         (634 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28055
          Length = 621

 Score = 1226 bits (3172), Expect = 0.0
 Identities = 580/634 (91%), Positives = 604/634 (95%), Gaps = 13/634 (2%)

Query: 1   MTIRSLPALSPLALSVRVLLLAGGLALGNVATAATAPAAPAAPAGKSVTWEDIANDHLTT 60
           M I++LPALS L ++   LLLAG L+L  +A AA       AP    V+WEDIANDHLTT
Sbjct: 1   MRIKTLPALSALTVA---LLLAGSLSLSPLANAA-------APG---VSWEDIANDHLTT 47

Query: 61  KDVLQYGMGTNAQRWSPLAQVNDQNVFKLTPAWSYSFGDEKQRGQESQAIVSDGVVYVTG 120
           +DVLQYGMGTNAQRWSPL QVND+NVFKLTPAWSYSFGDEKQRGQESQAIV DGVVYVTG
Sbjct: 48  QDVLQYGMGTNAQRWSPLVQVNDKNVFKLTPAWSYSFGDEKQRGQESQAIVRDGVVYVTG 107

Query: 121 SYSRVFALDAKTGKRLWTYNHRLPDNIRPCCDVVNRGAAIFGDKIYFGTLDARLIALDKH 180
           SYSRVFALDA+TGKRLWTYNHRLPDNIRPCCDVVNRGAAI+GDKIYFGTLDAR++ALDK+
Sbjct: 108 SYSRVFALDARTGKRLWTYNHRLPDNIRPCCDVVNRGAAIYGDKIYFGTLDARVVALDKN 167

Query: 181 TGKVVWNKKFGDHSAGYTMTGAPVLIKDKTSGKVLLIHGSSGDEFGVVGQLFARDPDTGE 240
           TGKVVWNKKFGDH+ GYTMTGAPVLIKDKTSGKVLLIHGSSGDEFGVVGQLFARDP+TGE
Sbjct: 168 TGKVVWNKKFGDHAGGYTMTGAPVLIKDKTSGKVLLIHGSSGDEFGVVGQLFARDPETGE 227

Query: 241 EVWMRPFVEGHMGRLNGKDSTPTGDVKAPSWPDDPTTETGKVEAWSHGGGAPWQSASFDP 300
           EVWMRPFVEGHMGRLNGKDSTPTGDVKAPSWPDD TTETGKVEAWSHGGGAPWQSASFD 
Sbjct: 228 EVWMRPFVEGHMGRLNGKDSTPTGDVKAPSWPDDKTTETGKVEAWSHGGGAPWQSASFDA 287

Query: 301 ETNTIIVGAGNPGPWNTWARTSKDGNPHDFDSLYTSGQVGVDPSTGEVKWFYQHTPNDAW 360
           ETNTIIVGAGNPGPWNTWART+KDGNPHD+DSLYTSGQVGVDPSTGEVKWFYQHTPNDAW
Sbjct: 288 ETNTIIVGAGNPGPWNTWARTAKDGNPHDYDSLYTSGQVGVDPSTGEVKWFYQHTPNDAW 347

Query: 361 DFSGNNELVLFDYKDKNGNVVKATAHADRNGFFYVVDRNNGKLQNAFPFVDNITWASHID 420
           DFSGNNELVLFDYKDK+G VVKATAHADRNGFFYVVDRNNGKLQNAFPFVDNITWASHID
Sbjct: 348 DFSGNNELVLFDYKDKDGKVVKATAHADRNGFFYVVDRNNGKLQNAFPFVDNITWASHID 407

Query: 421 LKTGRPVENPGQRPAKPLPGETKGKPVEVSPPFLGGKNWNPMAYSQDTGLFYIPGNQWKE 480
           LKTGRPVENPGQRPAKPLPGETKGKPVEVSPPFLGGKNWNPMAYSQDTGLFY+PGNQWKE
Sbjct: 408 LKTGRPVENPGQRPAKPLPGETKGKPVEVSPPFLGGKNWNPMAYSQDTGLFYVPGNQWKE 467

Query: 481 EYWTEEVNYKKGSAYLGMGFRIKRMYDDHVGTLRAMDPTTGKLVWEHKEHLPLWAGVLAT 540
           EYWTEEVNYKKGSAYLGMGFRIKRMYDDHVG+LRAM+PTTGK+VWEHKE LPLWAGVLAT
Sbjct: 468 EYWTEEVNYKKGSAYLGMGFRIKRMYDDHVGSLRAMNPTTGKVVWEHKEALPLWAGVLAT 527

Query: 541 KGNLVFTGTGDGFFKAFDAKTGKELWKFQTGSGIVSPPITWEQDGEQYIGVTVGYGGAVP 600
           KGNLVFTGTGDGFFKAFDAKTGKELWKFQTGSGIVSPPITWEQDGEQYIGVTVGYGGAVP
Sbjct: 528 KGNLVFTGTGDGFFKAFDAKTGKELWKFQTGSGIVSPPITWEQDGEQYIGVTVGYGGAVP 587

Query: 601 LWGGDMAELTKPVAQGGSFWVFKIPSWDNKTAQR 634
           LWGGDMAELTKPVAQGGSFWVFKIPSWD  TAQ+
Sbjct: 588 LWGGDMAELTKPVAQGGSFWVFKIPSWDKATAQK 621


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: 2130
Number of extensions: 146
Number of successful extensions: 15
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: 621
Length adjustment: 38
Effective length of query: 596
Effective length of database: 583
Effective search space:   347468
Effective search space used:   347468
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.

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Candidates (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

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