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 decanol dehydrogenase; EC 1.1.-.- (characterized)
to candidate GFF2017 Psest_2060 PQQ-dependent dehydrogenase, methanol/ethanol family

Query= CharProtDB::CH_107432
         (595 letters)



>FitnessBrowser__psRCH2:GFF2017
          Length = 592

 Score = 1016 bits (2626), Expect = 0.0
 Identities = 469/586 (80%), Positives = 534/586 (91%), Gaps = 1/586 (0%)

Query: 1   MTRSPRRPMFAVSLVLSAMLLAGAAHAAVSNEEILQDPKNPQQIVTNGLGVQGQRYSPLD 60
           M  +  R  FA++ + +A+ ++     AV+++EIL D K+  QIVTNG+G+QGQRYS LD
Sbjct: 1   MKHTGLRKPFALTALCAAVAMSSLHAWAVTDQEILNDAKSTDQIVTNGMGLQGQRYSTLD 60

Query: 61  LLNANNVKELRPVWAFSFGGEKQRGQQAQPLIKDGVMYLTGSYSRVFAVDARTGKKLWQY 120
            LNANN+ +LRPVW FS GGEKQRGQ+AQPLIKDGVMY+TGSYSRV+AVDARTGK+LWQY
Sbjct: 61  ALNANNINQLRPVWGFSLGGEKQRGQEAQPLIKDGVMYITGSYSRVYAVDARTGKELWQY 120

Query: 121 DARLPDDIRPCCDVINRGVALYGDLVFFGTLDAKLVALNKDTGKVVWSKKVADHKEGYSI 180
           DARLPD I PCCDVINRGVALY DLV FGTLDAKLVALNKDTGKVVW K VAD+K GYS+
Sbjct: 121 DARLPDGIMPCCDVINRGVALYDDLVIFGTLDAKLVALNKDTGKVVWKKTVADYKAGYSL 180

Query: 181 SAAPMIVNGKLITGVAGGEFGVVGKIQAYNPENGELLWMRPTVEGHMGYVYKDGKAIENG 240
           +AAP+IV GKLITGV+GGEFGVVGKI+AYNP+NGELLW RPTVEGHMGYV+KDGK +E+G
Sbjct: 181 TAAPLIVKGKLITGVSGGEFGVVGKIEAYNPKNGELLWTRPTVEGHMGYVWKDGKKVESG 240

Query: 241 ISGGEAGKTWPGDLWKTGGAAPWLGGYYDPETNLILFGTGNPAPWNSHLRPGDNLYSSSR 300
           ISGGEAGKTWPGDLWKTGGAAPWLGGYYDP+T+ +LFGTGNPAPWNSHLRPGDNLYSSSR
Sbjct: 241 ISGGEAGKTWPGDLWKTGGAAPWLGGYYDPDTDSLLFGTGNPAPWNSHLRPGDNLYSSSR 300

Query: 301 LALNPDDGTIKWHFQSTPHDGWDFDGVNELISFNYKDGGKEVKAAATADRNGFFYVLDRT 360
           LAL+P+DG+IKWHFQ+TPHDGWD+DGVNEL+SF+Y++GGK +KAA TADRNGFFYVLDRT
Sbjct: 301 LALDPNDGSIKWHFQTTPHDGWDYDGVNELVSFDYQEGGKTIKAAGTADRNGFFYVLDRT 360

Query: 361 NGKFIRGFPFVDKITWATGLDKDGRPIYNDASRPGAPG-SEAKGSSVFVAPAFLGAKNWM 419
           NGKFIRGFPFVDKITWA GLDK+GRPIY+DA+RPG+P  + A+G +V VAP+FLG KNWM
Sbjct: 361 NGKFIRGFPFVDKITWAKGLDKNGRPIYDDANRPGSPNDAGAQGKTVTVAPSFLGGKNWM 420

Query: 420 PMAYNKDTGLFYVPSNEWGMDIWNEGIAYKKGAAFLGAGFTIKPLNEDYIGVLRAIDPIS 479
           PMAY++DTGLFYVPSNEW MDIWNEG AYKKGAA+LGAGFTI PLN+DYIGVLRAIDP +
Sbjct: 421 PMAYSQDTGLFYVPSNEWSMDIWNEGTAYKKGAAYLGAGFTIHPLNDDYIGVLRAIDPKT 480

Query: 480 GKEVWRHKNYAPLWGGVLTTKGNLVFTGTPEGFLQAFNAKTGDKVWEFQTGSGVLGSPVT 539
           GKEVWR+KNYAPLWGGVL TKGNLVFTG PEG+L AF+AKTG K++EF TGSGV+GSPVT
Sbjct: 481 GKEVWRYKNYAPLWGGVLATKGNLVFTGNPEGYLMAFDAKTGKKLYEFNTGSGVIGSPVT 540

Query: 540 WEMDGEQYVSVVSGWGGAVPLWGGEVAKRVKDFNQGGMLWTFKLPK 585
           WEMDGEQYVSV+SGWGGAVPLWGGEVAKRVK+FNQGGM+WTFKLPK
Sbjct: 541 WEMDGEQYVSVLSGWGGAVPLWGGEVAKRVKEFNQGGMVWTFKLPK 586


Lambda     K      H
   0.317    0.137    0.438 

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: 1937
Number of extensions: 136
Number of successful extensions: 10
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: 595
Length of database: 592
Length adjustment: 37
Effective length of query: 558
Effective length of database: 555
Effective search space:   309690
Effective search space used:   309690
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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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