GapMind for catabolism of small carbon sources

 

Alignments 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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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:

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:

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:

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:

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