GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Burkholderia phytofirmans PsJN

Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate BPHYT_RS23020 BPHYT_RS23020 alcohol dehydrogenase

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



>FitnessBrowser__BFirm:BPHYT_RS23020
          Length = 451

 Score =  547 bits (1410), Expect = e-160
 Identities = 268/415 (64%), Positives = 313/415 (75%), Gaps = 2/415 (0%)

Query: 3   ALVIATLALLGSAAANAAEADQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMETPI 62
           A V+    L   AAA  +  D   L+  GEYLARAGDC+ACH+A  GKPFAGGL  +TPI
Sbjct: 20  AAVLGMTTLAAHAAAPQSRNDT-TLIAHGEYLARAGDCIACHSAPSGKPFAGGLKFDTPI 78

Query: 63  GVIYSTNITPDK-TGIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALY 121
           G IYSTNITPD+ TGIG ++F  FD+AVR GV   G TLYPAMPFPSYAR+S  DM ALY
Sbjct: 79  GAIYSTNITPDRSTGIGSWTFAQFDRAVRAGVKPNGDTLYPAMPFPSYARLSQDDMHALY 138

Query: 122 AYFMKGVAPVARDNQDSDIPWPLSMRWPLSIWRWMFAPSVETPAPAAGSDPVISRGAYLV 181
           AYF  GVAPV + N+  DI WPLSMRWPL IWR +FAP   +      +DPVI+RGAYLV
Sbjct: 139 AYFTHGVAPVNQKNKPVDIVWPLSMRWPLGIWRHLFAPEPVSFDAKRYADPVIARGAYLV 198

Query: 182 EGLGHCGACHTPRALTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSEEQ 241
           +GLGHCGACHTPRA TMQE+ALS   G  FL+G A ++GWI  SLRG+ + G+G+WSE  
Sbjct: 199 QGLGHCGACHTPRAATMQERALSEFDGPAFLAGGAAIDGWIPSSLRGNPRTGIGAWSEAD 258

Query: 242 LVQFLKTGRSDRSAVFGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKDQPHQYDKQ 301
           LVQFLKTGR+  SA FGGM+DVV HSMQ+M DADLTAIARYLK+LP+ DP++ P+ YD  
Sbjct: 259 LVQFLKTGRTQHSAAFGGMTDVVQHSMQHMNDADLTAIARYLKTLPSTDPQETPYAYDDT 318

Query: 302 VAQALWNGDDSKPGAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSADATSLIHIVLK 361
            A+AL  GD S PGAAVY DNC ACHR+DG GY RVFPAL GNPV+Q  DATSLIH++L 
Sbjct: 319 AARALRMGDASAPGAAVYRDNCTACHRSDGRGYNRVFPALGGNPVVQGKDATSLIHVLLT 378

Query: 362 GGTLPATHSAPSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGDVAALR 416
           G TL  T +APS+FTMPAF WRL+DQEVADV NF+R+SWGN  S V   DVA +R
Sbjct: 379 GSTLEGTKTAPSSFTMPAFGWRLNDQEVADVTNFVRTSWGNSGSTVSATDVAKVR 433


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: 713
Number of extensions: 35
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 434
Length of database: 451
Length adjustment: 32
Effective length of query: 402
Effective length of database: 419
Effective search space:   168438
Effective search space used:   168438
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