GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Paraburkholderia bryophila 376MFSha3.1

Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate H281DRAFT_03306 H281DRAFT_03306 Cytochrome c, mono- and diheme variants

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



>FitnessBrowser__Burk376:H281DRAFT_03306
          Length = 434

 Score =  343 bits (880), Expect = 6e-99
 Identities = 190/427 (44%), Positives = 251/427 (58%), Gaps = 15/427 (3%)

Query: 2   KALVIATLALLGSAA--------ANAAEADQQALVQQGEYLARAGDCVACHTAKDGKPFA 53
           K +V+A  A+LG+          A A++    ALV +GEYLA+A DC  CHTA  G+ + 
Sbjct: 6   KLIVLAGTAMLGAFTTPCVTAEPAGASDPALAALVARGEYLAKASDCAGCHTAVGGQAYG 65

Query: 54  GGLPMETPIGVIYSTNITPDKT-GIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARV 112
           GGL + +P G I S+NITPD+  GIG YS+EDF ++VR GV+ G   LYPAMP+ S++++
Sbjct: 66  GGLGLTSPFGTIMSSNITPDRRYGIGAYSYEDFARSVREGVSPGNKRLYPAMPYASFSKM 125

Query: 113 SDADMQALYAYFMKGVAPVARDNQDSDIPWPLSMRWPLSIWRWMFAPSVETPAPAAGSDP 172
           SD DM+ALYAYFM GV P       + + +P + RW L  W+  FAP+ E   P AG D 
Sbjct: 126 SDDDMRALYAYFMHGVKPAPEPAPPTKLAFPFNQRWVLYFWQLAFAPT-EPYRPKAGRDA 184

Query: 173 VISRGAYLVEGLGHCGACHTPRALTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKD 232
             +RGA+LV+G GHCGACHTPR    QE+    S    +L+G    + W   +L GD   
Sbjct: 185 QWNRGAFLVQGPGHCGACHTPRGPGFQERGYDESSPM-YLTGGVN-DNWFGPNLTGDPGS 242

Query: 233 GLGSWSEEQLVQFLKTGRSDRSAVFGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPK 292
           GLG   E+ L  FLKTG       FG M + V  S QY+TD D  A+A Y+KSLPA  P 
Sbjct: 243 GLGRIGEKDLAAFLKTGHGAGLVAFGSMVEQVEDSTQYLTDEDALAMAHYVKSLPAQKPS 302

Query: 293 D--QPH-QYDKQVAQALWNGDDSKPGAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQS 349
              +PH Q D               GA VYI  CA CH   G G   VFP LAGNP + +
Sbjct: 303 GSYEPHAQPDLPTRNGNRVDAPQSVGARVYISFCARCHGVQGAGMPNVFPRLAGNPSVIT 362

Query: 350 ADATSLIHIVLKGGTLPATHSAPSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKP 409
            D TSLI ++++GG  PAT S P    MP FA  L++ ++A+V+++IR+SWGN A  V  
Sbjct: 363 EDTTSLIRLMVEGGNSPATISGPPRQAMPGFAQTLTNAQMANVLSWIRTSWGNDARPVTA 422

Query: 410 GDVAALR 416
            D+ +LR
Sbjct: 423 NDIQSLR 429


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: 582
Number of extensions: 25
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: 434
Length of database: 434
Length adjustment: 32
Effective length of query: 402
Effective length of database: 402
Effective search space:   161604
Effective search space used:   161604
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