Alignments for a candidate for etoh-dh-c in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for etoh-dh-c in Pseudomonas stutzeri RCH2

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 GFF2011 Psest_2054 PQQ-dependent dehydrogenase, methanol/ethanol family

Query= SwissProt::A8R3S4
         (623 letters)



>FitnessBrowser__psRCH2:GFF2011
          Length = 623

 Score = 1158 bits (2996), Expect = 0.0
 Identities = 533/623 (85%), Positives = 578/623 (92%)

Query: 1   MTIRSLPAALSPLSMAVQAVLLVSSLALAPAANAKPVTWEDIANDHLNTQNVLQYGMGTN 60
           MT RS P +  PL++AV  + L  SLALA AA+AKPV+WEDIANDHL+T NVLQYGMGTN
Sbjct: 1   MTTRSNPGSKRPLAIAVHYLALAGSLALAGAAHAKPVSWEDIANDHLSTANVLQYGMGTN 60

Query: 61  AQRWSPLAMVNDKNVFKLTPAWSYSFGDERQRGQESQAIINDGVIYVTGSYSRVFALDAK 120
           AQRWSPLA VN+ NVFKLTPAWS+SFGDE+QRGQESQAI++DGVIYVTGSYSRVFALDAK
Sbjct: 61  AQRWSPLAQVNESNVFKLTPAWSFSFGDEKQRGQESQAIVHDGVIYVTGSYSRVFALDAK 120

Query: 121 TGRRLWTYNHRLPDNIRPCCDVVNRGAAIFGDKIYFGTLDARVIALNKDTGKVVWNKKFG 180
           TG+RLW+Y HRLPD+IRPCCDVVNRGAAI+GDKIYFGTLDARV+ALNKDTGKVVWNKKFG
Sbjct: 121 TGKRLWSYAHRLPDDIRPCCDVVNRGAAIYGDKIYFGTLDARVVALNKDTGKVVWNKKFG 180

Query: 181 DHSAGYTMTGAPTLIKDQKSGKVLLIHGSSGDEFGVVGQLYARDPETGEEVWMRPFVEGH 240
           DH+AGYTMTGAPTL+KD K+GKVLL+HGSSGDEFG+VG+L+ARDPETGEEVWMRPFVEGH
Sbjct: 181 DHAAGYTMTGAPTLVKDGKTGKVLLVHGSSGDEFGIVGKLFARDPETGEEVWMRPFVEGH 240

Query: 241 MGRLNGKDSTPTGDVKAPSWPDDPTTETGKVESWSHGGGAPWQSASFDPETNTIIVGAGN 300
           MGRLNGKDSTPTGD+KAPSWPDDP   TGK E+WS GGGAPWQSASFDPETNTIIVGAGN
Sbjct: 241 MGRLNGKDSTPTGDIKAPSWPDDPNHPTGKKEAWSQGGGAPWQSASFDPETNTIIVGAGN 300

Query: 301 PGPWNTWARTSKDGNPHDFDSLYTSGQVGVDPTTGEVKWFYQHTPNDAWDFSGNNELVLF 360
           P PWN W RTS  GNP D+DSLYTSGQVGVDP+TGEVKWFYQHTPNDAWDFSGNNELVLF
Sbjct: 301 PAPWNGWERTSDGGNPKDYDSLYTSGQVGVDPSTGEVKWFYQHTPNDAWDFSGNNELVLF 360

Query: 361 DYKDKDGKQYKATAHADRNGFFYVVDRTNGKLKNAFPFVDNITWASHIDLKTGRPVENEG 420
           DYKD +GK  KATAHADRNGFFYVVDR +GKL+NAFPFVD ITWASHIDLKTGRPVEN+G
Sbjct: 361 DYKDNNGKTVKATAHADRNGFFYVVDRKDGKLQNAFPFVDGITWASHIDLKTGRPVENQG 420

Query: 421 QRPAKPLPGETKGKPVEVSPPFLGGKNWNPMAYSQDTGLFYVPANHWKEEYWTEEVNYKK 480
           QRP KP PGE  GK VEVSPPFLGGKNWNPMAYSQDTGLFYVPANHWKE+YWTEEV+YKK
Sbjct: 421 QRPPKPEPGEKHGKSVEVSPPFLGGKNWNPMAYSQDTGLFYVPANHWKEDYWTEEVSYKK 480

Query: 481 GSAYLGIGFRIKRMYEDHVGSLRAMDPTTGKVVWEHNERLPLWAGVLATKGNLVFTGTGD 540
           GSAYLG GFRIKRMY+DHVG LRAM+PTTGK+ WEH E+LPLWAGVLATKGNL+FTGT D
Sbjct: 481 GSAYLGQGFRIKRMYDDHVGILRAMNPTTGKIEWEHKEKLPLWAGVLATKGNLIFTGTSD 540

Query: 541 GYFKAFNAKTGEELWKFQTGSGIVSPPITWEQDGEQYIGVTVGYGGAVPLWGGDMAELTK 600
           GYFKAFNAKTG+ELWKFQTGSG++SPP+TWEQDGEQYIGVTVGYGGAVPLWGGDMA LTK
Sbjct: 541 GYFKAFNAKTGDELWKFQTGSGVISPPVTWEQDGEQYIGVTVGYGGAVPLWGGDMAVLTK 600

Query: 601 PVAQGGSFWVFKIPAWDTKTAKR 623
           PVAQGGSFWVFK+P W+ KTAKR
Sbjct: 601 PVAQGGSFWVFKLPEWEKKTAKR 623


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: 2132
Number of extensions: 147
Number of successful extensions: 9
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: 623
Length adjustment: 37
Effective length of query: 586
Effective length of database: 586
Effective search space:   343396
Effective search space used:   343396
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