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 decanol dehydrogenase; EC 1.1.-.- (characterized)
to candidate GFF3218 HP15_3160 quinoprotein alcohol dehydrogenase

Query= CharProtDB::CH_107432
         (595 letters)



>FitnessBrowser__Marino:GFF3218
          Length = 591

 Score =  914 bits (2362), Expect = 0.0
 Identities = 419/584 (71%), Positives = 501/584 (85%), Gaps = 4/584 (0%)

Query: 6   RRPMFAVSLVLSAMLLAGAAHA-AVSNEEILQDPKNPQQIVTNGLGVQGQRYSPLDLLNA 64
           R   F + +  SA+ +A +  A AV++E+I+ D K P+ IV+ G+G QGQRYS L+ LN 
Sbjct: 2   RTNKFGIRIAASALAMAVSYGAHAVTDEDIINDHKTPEDIVSYGMGTQGQRYSILEDLNT 61

Query: 65  NNVKELRPVWAFSFGGEKQRGQQAQPLIKDGVMYLTGSYSRVFAVDARTGKKLWQYDARL 124
           +NV+ L+P WAFSFG EK RGQ++QPLIKDGVMY+T SYSR++A+DARTG+++WQYDARL
Sbjct: 62  SNVQYLQPAWAFSFGSEKMRGQESQPLIKDGVMYVTASYSRIYAIDARTGEEIWQYDARL 121

Query: 125 PDDIRPCCDVINRGVALYGDLVFFGTLDAKLVALNKDTGKVVWSKKVADHKEGYSISAAP 184
           PD I PCCDV+NRG A+YGD V FGTLDAKLVALNKDTGK +W KKVAD++ GY+I+AAP
Sbjct: 122 PDGIMPCCDVVNRGAAIYGDKVIFGTLDAKLVALNKDTGKPMWIKKVADYQAGYAITAAP 181

Query: 185 MIVNGKLITGVAGGEFGVVGKIQAYNPENGELLWMRPTVEGHMGYVYKDGKAIENGISGG 244
           M++ GK+ITGV+GGEFG+VGK++AY+   G+L+W RPTVEGHMGYVYKDGK IENGISGG
Sbjct: 182 MVIKGKVITGVSGGEFGIVGKVEAYDANTGDLVWTRPTVEGHMGYVYKDGKKIENGISGG 241

Query: 245 EAGKTWPGDLWKTGGAAPWLGGYYDPETNLILFGTGNPAPWNSHLRPGDNLYSSSRLALN 304
           +AG TWPG++WK GGAA WLGG YDP+T+ + FGTGNPAPWNSHLRPGDNL+SSSRLA++
Sbjct: 242 KAGVTWPGEMWKNGGAATWLGGTYDPDTDSLFFGTGNPAPWNSHLRPGDNLFSSSRLAID 301

Query: 305 PDDGTIKWHFQSTPHDGWDFDGVNELISFNYKDGGKEVKAAATADRNGFFYVLDRTNGKF 364
           PDDG+IKWHFQ+TP+DGWD+DGVNELISF+Y++ GK VKAAATADRNGFFYVL+R NG F
Sbjct: 302 PDDGSIKWHFQTTPNDGWDYDGVNELISFDYEENGKTVKAAATADRNGFFYVLNRENGDF 361

Query: 365 IRGFPFVDKITWATGLD-KDGRPIYNDASRPGAPG--SEAKGSSVFVAPAFLGAKNWMPM 421
           IRGFPFVDKITWA GLD K GRPIY +  RPG P      KG  V   PAFLG KNWMPM
Sbjct: 362 IRGFPFVDKITWAEGLDPKTGRPIYAEGGRPGNPADMEGGKGEMVLAQPAFLGGKNWMPM 421

Query: 422 AYNKDTGLFYVPSNEWGMDIWNEGIAYKKGAAFLGAGFTIKPLNEDYIGVLRAIDPISGK 481
           A+++ TGLFYVPSNEW MDIWNE ++YKKGAAFLGAGFTIKP N+DYIGVLRA+DP +G+
Sbjct: 422 AFSQQTGLFYVPSNEWSMDIWNEPVSYKKGAAFLGAGFTIKPANDDYIGVLRAMDPKTGE 481

Query: 482 EVWRHKNYAPLWGGVLTTKGNLVFTGTPEGFLQAFNAKTGDKVWEFQTGSGVLGSPVTWE 541
           EVWR++N APLWGGV+TT G LVFTGTPEG L+AF+AKTG++++ F TGSGV+G+P+TW 
Sbjct: 482 EVWRYENTAPLWGGVMTTAGGLVFTGTPEGHLKAFDAKTGEELYRFNTGSGVVGTPITWT 541

Query: 542 MDGEQYVSVVSGWGGAVPLWGGEVAKRVKDFNQGGMLWTFKLPK 585
           MDGEQYVSV SGWGGAVPLWGGEVAK VKDFNQGGM+WTFKLPK
Sbjct: 542 MDGEQYVSVASGWGGAVPLWGGEVAKVVKDFNQGGMVWTFKLPK 585


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: 1810
Number of extensions: 131
Number of successful extensions: 13
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: 591
Length adjustment: 37
Effective length of query: 558
Effective length of database: 554
Effective search space:   309132
Effective search space used:   309132
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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Steps (tab-delimited)
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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