Alignments for a candidate for etoh-dh-c in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for etoh-dh-c in Marinobacter adhaerens HP15

Align Quinoprotein alcohol dehydrogenase (cytochrome c); Quinoprotein alcohol dehydrogenase (cytochrome c550); Quinoprotein alcohol dehydrogenase ADH I; ADH I; Quinoprotein ethanol dehydrogenase; QEDH; EC 1.1.2.8 (characterized)
to candidate GFF3222 HP15_3164 quinoprotein alcohol dehydrogenase

Query= SwissProt::A8R3S4
         (623 letters)



>FitnessBrowser__Marino:GFF3222
          Length = 617

 Score =  993 bits (2568), Expect = 0.0
 Identities = 458/606 (75%), Positives = 520/606 (85%), Gaps = 3/606 (0%)

Query: 12  PLSMAVQAVLLVSSLA-LAPAANAKPVTWEDIANDHLNTQNVLQYGMGTNAQRWSPLAMV 70
           PL   +   L +SS A LA   +AK VTW+DIAND    +NVL YG+G  AQR+SP+  +
Sbjct: 9   PLLRGIGLALALSSAAGLASQVHAKDVTWDDIANDAQTPENVLGYGIGPKAQRYSPMTTI 68

Query: 71  NDKNVFKLTPAWSYSFGDERQRGQESQAIINDGVIYVTGSYSRVFALDAKTGRRLWTYNH 130
           N  NV +L PAWS+SFGDE+QRGQESQA+++DGV+YVTGSYSR+FALDAKTG RLW Y+H
Sbjct: 69  NRDNVERLVPAWSFSFGDEKQRGQESQALVHDGVVYVTGSYSRLFALDAKTGERLWEYSH 128

Query: 131 RLPDNIRPCCDVVNRGAAIFGDKIYFGTLDARVIALNKDTGKVVWNKKFGDHSAGYTMTG 190
           RLP+ IRPCCDVVNRGAAIFGDK++FGTLDA ++ALNKDTGKVVW +KF DH AGYTMTG
Sbjct: 129 RLPEGIRPCCDVVNRGAAIFGDKVFFGTLDAGIVALNKDTGKVVWREKFADHEAGYTMTG 188

Query: 191 APTLIKDQKSGKVLLIHGSSGDEFGVVGQLYARDPETGEEVWMRPFVEGHMGRLNGKDST 250
           APTL+KDQK+ +         DEFGVVG+L+ARDP+TG+E+WMRPFVEGH GRLNG+ ST
Sbjct: 189 APTLVKDQKNRQGTADSRLLRDEFGVVGKLFARDPDTGKEIWMRPFVEGHYGRLNGEKST 248

Query: 251 PTGDVKAPSWPDDPTTETGKVESWSHGGGAPWQSASFDPETNTIIVGAGNPGPWNTWART 310
           PTGD +APSWPDDP TETGKVE+WSHGGGAPWQSASFD ETNTII+GAGNP PWNTW RT
Sbjct: 249 PTGDPRAPSWPDDPNTETGKVEAWSHGGGAPWQSASFDAETNTIIIGAGNPAPWNTWKRT 308

Query: 311 SKDGNPHDFDSLYTSGQVGVDPTTGEVKWFYQHTPNDAWDFSGNNELVLFDYKDKDGKQY 370
           S  G+P D+D+LYTSGQVGVDPTTGEVKWFYQHTPNDAWDFSGNNELVLF+Y D++G+  
Sbjct: 309 SPGGDPADYDNLYTSGQVGVDPTTGEVKWFYQHTPNDAWDFSGNNELVLFEY-DENGETV 367

Query: 371 KATAHADRNGFFYVVDRTNGKLKNAFPFVDNITWASHIDLKTGRPVENEGQRPAKPLPGE 430
           KATAHADRNGFFYVVDR NG+ K  FPFVDNITWA  I    GRPVE +GQRP     GE
Sbjct: 368 KATAHADRNGFFYVVDRENGEFKKGFPFVDNITWAERIG-DDGRPVERKGQRPPPVAQGE 426

Query: 431 TKGKPVEVSPPFLGGKNWNPMAYSQDTGLFYVPANHWKEEYWTEEVNYKKGSAYLGIGFR 490
           T+G+ +EVSPPFLGGKNWNPMAYSQDTGLFYVPANHWKE+YWTEEV YKKG+AYLG GFR
Sbjct: 427 TRGEAIEVSPPFLGGKNWNPMAYSQDTGLFYVPANHWKEDYWTEEVTYKKGAAYLGQGFR 486

Query: 491 IKRMYEDHVGSLRAMDPTTGKVVWEHNERLPLWAGVLATKGNLVFTGTGDGYFKAFNAKT 550
           IKRMY+DHVG LRAM+P TG++ WEH ERLPLWAGVL TKG LVFTGTGDG+ KAF+A+T
Sbjct: 487 IKRMYDDHVGILRAMNPLTGEIEWEHKERLPLWAGVLTTKGGLVFTGTGDGFLKAFDAET 546

Query: 551 GEELWKFQTGSGIVSPPITWEQDGEQYIGVTVGYGGAVPLWGGDMAELTKPVAQGGSFWV 610
           GEELWKFQTGSGI+S PITWE DGEQYIGV  GYGGAVPLWGGDMAELTKP++QGGSFWV
Sbjct: 547 GEELWKFQTGSGIISSPITWEMDGEQYIGVASGYGGAVPLWGGDMAELTKPISQGGSFWV 606

Query: 611 FKIPAW 616
           FK+P+W
Sbjct: 607 FKMPSW 612


Lambda     K      H
   0.316    0.135    0.432 

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: 1967
Number of extensions: 148
Number of successful extensions: 16
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: 623
Length of database: 617
Length adjustment: 37
Effective length of query: 586
Effective length of database: 580
Effective search space:   339880
Effective search space used:   339880
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: 53 (25.0 bits)

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

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Protein sequences (fasta format)
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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