Aligments for a candidate for gadh2 in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for gadh2 in Pseudomonas simiae WCS417

Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate GFF53 PS417_00270 alcohol dehydrogenase

Query= metacyc::MONOMER-12746
         (434 letters)



>FitnessBrowser__WCS417:GFF53
          Length = 420

 Score =  725 bits (1872), Expect = 0.0
 Identities = 351/416 (84%), Positives = 378/416 (90%), Gaps = 3/416 (0%)

Query: 1   MKALVIATLALLGSAAANAAEADQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMET 60
           MKALVIAT AL  S + +AAE D   L++QGEYLARAGDCVACHTAK GKPFAGGLPMET
Sbjct: 1   MKALVIATFALFSSCSVSAAETD---LIKQGEYLARAGDCVACHTAKGGKPFAGGLPMET 57

Query: 61  PIGVIYSTNITPDKTGIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQAL 120
           PIGVIYSTNITPDKTG+GDYSFEDFDKAVRHGVAK GSTLYPAMP+PSYARVSD+DMQAL
Sbjct: 58  PIGVIYSTNITPDKTGLGDYSFEDFDKAVRHGVAKSGSTLYPAMPYPSYARVSDSDMQAL 117

Query: 121 YAYFMKGVAPVARDNQDSDIPWPLSMRWPLSIWRWMFAPSVETPAPAAGSDPVISRGAYL 180
           YAYFMKGV PVA++N+DSDIPWPLSMRWPL+ WRWMFAP+VE     A  DPVISRGAYL
Sbjct: 118 YAYFMKGVEPVAQENKDSDIPWPLSMRWPLAAWRWMFAPAVEEHQAQAVVDPVISRGAYL 177

Query: 181 VEGLGHCGACHTPRALTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSEE 240
           VEGLGHCGACHTPRALTMQEKALSA+ G+ FL+GSAPLEGWIAKSLRGDHKDGLGSWSEE
Sbjct: 178 VEGLGHCGACHTPRALTMQEKALSATDGNAFLAGSAPLEGWIAKSLRGDHKDGLGSWSEE 237

Query: 241 QLVQFLKTGRSDRSAVFGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKDQPHQYDK 300
           QLVQFLKTGRSDRSAVFGGMSDVVVHSMQYM++ DLTAIARYLKSLPA DPKD PH YDK
Sbjct: 238 QLVQFLKTGRSDRSAVFGGMSDVVVHSMQYMSENDLTAIARYLKSLPAVDPKDSPHTYDK 297

Query: 301 QVAQALWNGDDSKPGAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSADATSLIHIVL 360
           QVA+ALW GDDS+ GA+VYIDNCAACHRTDGHGYTRVFPALAGNPVLQ+ADATSLI+IVL
Sbjct: 298 QVAEALWKGDDSQRGASVYIDNCAACHRTDGHGYTRVFPALAGNPVLQTADATSLINIVL 357

Query: 361 KGGTLPATHSAPSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGDVAALR 416
            GGTLPATH+APSTFTMPAFAWRLSDQEVADVV+F+R SWGN   A+    VA +R
Sbjct: 358 NGGTLPATHTAPSTFTMPAFAWRLSDQEVADVVSFVRGSWGNTGGAISAAQVADIR 413


Lambda     K      H
   0.316    0.131    0.404 

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: 780
Number of extensions: 30
Number of successful extensions: 2
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: 434
Length of database: 420
Length adjustment: 32
Effective length of query: 402
Effective length of database: 388
Effective search space:   155976
Effective search space used:   155976
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: 51 (24.3 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, or view the source code.

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