GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Cupriavidus basilensis 4G11

Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate RR42_RS10775 RR42_RS10775 alcohol dehydrogenase

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



>FitnessBrowser__Cup4G11:RR42_RS10775
          Length = 434

 Score =  392 bits (1006), Expect = e-113
 Identities = 197/415 (47%), Positives = 263/415 (63%), Gaps = 4/415 (0%)

Query: 3   ALVIATLALLGSAAANAAEADQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMETPI 62
           A V   + LL    A AA+A   A V++G YLA+  +C ACHT+  G PFAGGLP++T +
Sbjct: 10  ATVAFAVLLLAPCFAAAADAPGAAQVERGRYLAKVANCAACHTSVGGAPFAGGLPLKTGV 69

Query: 63  GVIYSTNITPD-KTGIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALY 121
           G +YSTNITPD  +GIG YSFE+FD+A+R GVA+ G  LYPAMP+PSYAR+++ D+QALY
Sbjct: 70  GTVYSTNITPDVDSGIGAYSFEEFDRALREGVARHGKRLYPAMPYPSYARLAEPDVQALY 129

Query: 122 AYFMKGVAPVARDNQDSDIPWPLSMRWPLSIWRWMFAPSVETPAPAAGSDPVISRGAYLV 181
           AY    V  V +   + ++ WP  MRW L +W W+F  S   PA A G     +RGAYLV
Sbjct: 130 AYLRTEVKAVRQATAEPEMRWPFGMRWLLRVWNWLFLESGPVPANA-GQSVEWNRGAYLV 188

Query: 182 EGLGHCGACHTPRALTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSEEQ 241
           + + HCGACHTPR + M EK L       FL+G A +EGW + +LRGD + GLG+WS E 
Sbjct: 189 QAVAHCGACHTPRGMLMAEKGLDERS-RHFLAG-ASVEGWASTNLRGDPRTGLGTWSRED 246

Query: 242 LVQFLKTGRSDRSAVFGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKDQPHQYDKQ 301
           + ++L TGR+  +  FG MS+V+  S Q+MT  DL A+A YLKS+P     + P+ YD  
Sbjct: 247 IAEYLHTGRNAHATSFGPMSEVIASSTQFMTRPDLDAVAVYLKSVPGARSDETPYAYDAH 306

Query: 302 VAQALWNGDDSKPGAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSADATSLIHIVLK 361
            A AL  G     GA  Y + C  CH  +G G+ RVFP LAGNP +   D +SL +++L 
Sbjct: 307 TADALAQGRFDATGARQYAEFCMPCHGANGKGFARVFPPLAGNPTVVDPDPSSLANLLLD 366

Query: 362 GGTLPATHSAPSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGDVAALR 416
           G       +A + + MP + W L +QE+A+V+ FIR+ WGNQAS VK   VAA R
Sbjct: 367 GAVTAHVGTAATDYHMPGYGWTLDNQELANVLTFIRTGWGNQASQVKEATVAARR 421


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: 549
Number of extensions: 32
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