Alignments for a candidate for etoh-dh-c in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for etoh-dh-c in Pseudomonas fluorescens FW300-N2E2

Align quinoprotein phenylethanol dehydrogenase; EC 1.1.-.- (characterized)
to candidate Pf6N2E2_1389 Quino(hemo)protein alcohol dehydrogenase, PQQ-dependent (EC 1.1.99.8)

Query= CharProtDB::CH_107431
         (634 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1389
          Length = 618

 Score = 1226 bits (3173), Expect = 0.0
 Identities = 582/634 (91%), Positives = 604/634 (95%), Gaps = 16/634 (2%)

Query: 1   MTIRSLPALSPLALSVRVLLLAGGLALGNVATAATAPAAPAAPAGKSVTWEDIANDHLTT 60
           M I++LPALS L ++   LLLAG L+        T+P A AA     VTWEDIANDHLTT
Sbjct: 1   MRIKTLPALSSLTVA---LLLAGSLS--------TSPLARAA-----VTWEDIANDHLTT 44

Query: 61  KDVLQYGMGTNAQRWSPLAQVNDQNVFKLTPAWSYSFGDEKQRGQESQAIVSDGVVYVTG 120
           +DVLQYGMGTNAQRWSPLAQVND+NVFKLTPAWSYSFGDEKQRGQESQAIVSDGVVYVTG
Sbjct: 45  QDVLQYGMGTNAQRWSPLAQVNDKNVFKLTPAWSYSFGDEKQRGQESQAIVSDGVVYVTG 104

Query: 121 SYSRVFALDAKTGKRLWTYNHRLPDNIRPCCDVVNRGAAIFGDKIYFGTLDARLIALDKH 180
           SYSRVFALDAKTGKRLWTYNHRLPDNIRPCCDVVNRGAAI+GDKIYFGTLDAR++ALDK+
Sbjct: 105 SYSRVFALDAKTGKRLWTYNHRLPDNIRPCCDVVNRGAAIYGDKIYFGTLDARVVALDKN 164

Query: 181 TGKVVWNKKFGDHSAGYTMTGAPVLIKDKTSGKVLLIHGSSGDEFGVVGQLFARDPDTGE 240
           TGKVVWNKKFGDH+ GYTMTGAPVLIKDKTSGKVLLIHGSSGDEFGVVGQLFARDPDTGE
Sbjct: 165 TGKVVWNKKFGDHAGGYTMTGAPVLIKDKTSGKVLLIHGSSGDEFGVVGQLFARDPDTGE 224

Query: 241 EVWMRPFVEGHMGRLNGKDSTPTGDVKAPSWPDDPTTETGKVEAWSHGGGAPWQSASFDP 300
           EVWMRPFVEGHMGRLNGKDSTPTGDVKAPSWPDD TTETGKVEAWSHGGGAPWQSASFD 
Sbjct: 225 EVWMRPFVEGHMGRLNGKDSTPTGDVKAPSWPDDKTTETGKVEAWSHGGGAPWQSASFDA 284

Query: 301 ETNTIIVGAGNPGPWNTWARTSKDGNPHDFDSLYTSGQVGVDPSTGEVKWFYQHTPNDAW 360
           ETNTIIVGAGNPGPWNTWART+KDGNPHD+DSLYTSGQVGVDPSTGEVKWFYQHTPNDAW
Sbjct: 285 ETNTIIVGAGNPGPWNTWARTAKDGNPHDYDSLYTSGQVGVDPSTGEVKWFYQHTPNDAW 344

Query: 361 DFSGNNELVLFDYKDKNGNVVKATAHADRNGFFYVVDRNNGKLQNAFPFVDNITWASHID 420
           DFSGNNELVLFDYKDK+G VVKATAHADRNGFFYVVDRNNGKLQNAFPFVDNITWASHID
Sbjct: 345 DFSGNNELVLFDYKDKDGKVVKATAHADRNGFFYVVDRNNGKLQNAFPFVDNITWASHID 404

Query: 421 LKTGRPVENPGQRPAKPLPGETKGKPVEVSPPFLGGKNWNPMAYSQDTGLFYIPGNQWKE 480
           LKTGRPVEN GQRPAKPLPGETKGKPVEVSPPFLGGKNWNPMAYSQDTGLFY+PGNQWKE
Sbjct: 405 LKTGRPVENAGQRPAKPLPGETKGKPVEVSPPFLGGKNWNPMAYSQDTGLFYVPGNQWKE 464

Query: 481 EYWTEEVNYKKGSAYLGMGFRIKRMYDDHVGTLRAMDPTTGKLVWEHKEHLPLWAGVLAT 540
           EYWTEEVNYKKGSAYLGMGFRIKRMYDDHVG+LRAM+PTTGK+VWEHKE LPLWAGVLAT
Sbjct: 465 EYWTEEVNYKKGSAYLGMGFRIKRMYDDHVGSLRAMNPTTGKVVWEHKEPLPLWAGVLAT 524

Query: 541 KGNLVFTGTGDGFFKAFDAKTGKELWKFQTGSGIVSPPITWEQDGEQYIGVTVGYGGAVP 600
           KGNLVFTGTGDGFFKAFDAKTGKELWKFQTGSGIVSPPITWEQDGEQ+IGVTVGYGGAVP
Sbjct: 525 KGNLVFTGTGDGFFKAFDAKTGKELWKFQTGSGIVSPPITWEQDGEQFIGVTVGYGGAVP 584

Query: 601 LWGGDMAELTKPVAQGGSFWVFKIPSWDNKTAQR 634
           LWGGDMAELTKPVAQGGSFWVFKIPSWD  TAQ+
Sbjct: 585 LWGGDMAELTKPVAQGGSFWVFKIPSWDKATAQK 618


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: 2121
Number of extensions: 148
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: 618
Length adjustment: 38
Effective length of query: 596
Effective length of database: 580
Effective search space:   345680
Effective search space used:   345680
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)
Steps (tab-delimited)
Rules (tab-delimited)
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