Aligments for a candidate for gadh2 in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Aligments for a candidate for gadh2 in Pseudomonas putida KT2440

Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate PP_3382 PP_3382 gluconate 2-dehydrogenase cytochrome c subunit

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



>FitnessBrowser__Putida:PP_3382
          Length = 417

 Score =  685 bits (1767), Expect = 0.0
 Identities = 333/416 (80%), Positives = 367/416 (88%), Gaps = 1/416 (0%)

Query: 1   MKALVIATLALLGSAAANAAEADQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMET 60
           MK L+IATL +LG+ AA  A A+  A V+ GEYLARAGDCVACHTAK GKPFAGGLPMET
Sbjct: 3   MKTLLIATL-VLGAGAAAQAVANDDAQVRLGEYLARAGDCVACHTAKGGKPFAGGLPMET 61

Query: 61  PIGVIYSTNITPDKTGIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQAL 120
           PIG +YSTNITP  +GIG YSFEDFD+AVR G+ K GSTLYPAMP+PSYARVS+ DMQAL
Sbjct: 62  PIGTVYSTNITPAASGIGQYSFEDFDQAVRRGIGKDGSTLYPAMPYPSYARVSEQDMQAL 121

Query: 121 YAYFMKGVAPVARDNQDSDIPWPLSMRWPLSIWRWMFAPSVETPAPAAGSDPVISRGAYL 180
           YAYFMKGVAPV + N+ SDIPWPLSMRWPL+IWR +FAP  +    +A +DPV++RGAYL
Sbjct: 122 YAYFMKGVAPVEQANKASDIPWPLSMRWPLAIWRGVFAPEAKPWQASATADPVVNRGAYL 181

Query: 181 VEGLGHCGACHTPRALTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSEE 240
           VEGLGHCGACHTPRALTMQEKALSA+ G  FL+GSAPLEGWIAK+LRGDHKDGLGSWSE 
Sbjct: 182 VEGLGHCGACHTPRALTMQEKALSAADGEQFLAGSAPLEGWIAKNLRGDHKDGLGSWSEA 241

Query: 241 QLVQFLKTGRSDRSAVFGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKDQPHQYDK 300
           QLVQFLKTGRSDRSAVFGGMSDVV HSMQ+M+DADLTAIARYLK+LP ++P DQ H YDK
Sbjct: 242 QLVQFLKTGRSDRSAVFGGMSDVVEHSMQHMSDADLTAIARYLKTLPPSNPDDQLHVYDK 301

Query: 301 QVAQALWNGDDSKPGAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSADATSLIHIVL 360
           QVA ALW GDDSKPGAAVYIDNCAACHRTDG GYTRVFPALAGNPV+Q+ADATSLIH+VL
Sbjct: 302 QVADALWKGDDSKPGAAVYIDNCAACHRTDGQGYTRVFPALAGNPVVQTADATSLIHVVL 361

Query: 361 KGGTLPATHSAPSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGDVAALR 416
            GGT+PATHSAPS FTMPAF WRLSDQEVA+VVNFIRSSWGNQ SAV  GDV +LR
Sbjct: 362 AGGTVPATHSAPSNFTMPAFGWRLSDQEVAEVVNFIRSSWGNQGSAVTAGDVKSLR 417


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: 736
Number of extensions: 26
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: 417
Length adjustment: 32
Effective length of query: 402
Effective length of database: 385
Effective search space:   154770
Effective search space used:   154770
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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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