Alignments for a candidate for etoh-dh-nad in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for etoh-dh-nad in Dinoroseobacter shibae DFL-12

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate 3607390 Dshi_0804 glucose-methanol-choline oxidoreductase (RefSeq)

Query= BRENDA::Q76HN6
         (526 letters)



>FitnessBrowser__Dino:3607390
          Length = 540

 Score =  476 bits (1226), Expect = e-139
 Identities = 250/528 (47%), Positives = 331/528 (62%), Gaps = 6/528 (1%)

Query: 1   MEFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNW 60
           ME DY+++GAGSAGCV+ANRLS D    V LLEAGP D +P IH P+G    +    V+W
Sbjct: 1   MEADYVVIGAGSAGCVVANRLSTDARNKVVLLEAGPPDTNPWIHIPVGYFKTMHNPTVDW 60

Query: 61  AFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLP 120
            +KT   PGL GR    PRGKVLGGSSS+NG++Y+RG  +D++ W+ +GN GWG+DDVLP
Sbjct: 61  CYKTQADPGLNGRSIDWPRGKVLGGSSSLNGLLYVRGQPEDYDRWRQMGNAGWGWDDVLP 120

Query: 121 YFRKSEMHHGGSSEYHGGDGELYVSPAN-RHAASEAFVESALRAGHSYNPDFNGATQEGA 179
            FR++E +  G+  +HG DG L VS    +    +A+V +A   G+ +NPD+NGA+QEG 
Sbjct: 121 LFRRAEANERGADPWHGDDGPLAVSNMRIQRPICDAWVAAAQAMGYPFNPDYNGASQEGV 180

Query: 180 GYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVH 239
           GY+ +T R+GRR S A A+LKP R R NL+++T   V  I + GK+ TGV     G R H
Sbjct: 181 GYFQLTTRNGRRCSAAVAYLKPARKRPNLSIITRALVTRIEMEGKRVTGVTYTDAGGRAH 240

Query: 240 -LRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCY 298
            + AR+EVILS GA  SPH+LMLSGIG   +L+  GI PRH LPGVG+NLQDH    L +
Sbjct: 241 TVSARREVILSGGAINSPHILMLSGIGDPDQLQAHGITPRHALPGVGKNLQDHLQARLVF 300

Query: 299 KSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSV 358
           K N+ + L   +   V   +    YA  R GP+    + A  FLKT P +  PDIQ H  
Sbjct: 301 KCNEPT-LNDEVRSLVNQARIALKYALFRAGPMTMAASLATGFLKTRPDIATPDIQFHVQ 359

Query: 359 IGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLL 418
             + D     +H    F+  VC LRP+S G + LA PDPR  P I PN+L+ + D ATL 
Sbjct: 360 PWSADSPGEGVHPFSAFTMSVCQLRPESRGEIRLAGPDPRTYPTIHPNYLSTETDCATLT 419

Query: 419 KGYRITRDIIAQTPMA---SFGLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQD 475
           +G +I R I    P+A   +   R   +  L +D   ++  R  + +IYHP GTCKMG  
Sbjct: 420 EGVKIARRIARADPLAGKIAEEFRPPANLALDDDAATLDWARSNSVSIYHPTGTCKMGTG 479

Query: 476 EMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523
             AVVD++LRVHG+ GLRV D SIMP +V GNTNA AIMI E+ ++ +
Sbjct: 480 PGAVVDARLRVHGLSGLRVADCSIMPEIVSGNTNAPAIMIGEKLSDMV 527


Lambda     K      H
   0.319    0.137    0.419 

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: 822
Number of extensions: 34
Number of successful extensions: 5
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: 526
Length of database: 540
Length adjustment: 35
Effective length of query: 491
Effective length of database: 505
Effective search space:   247955
Effective search space used:   247955
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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