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_04220 H281DRAFT_04220 Cytochrome c, mono- and diheme variants

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



>FitnessBrowser__Burk376:H281DRAFT_04220
          Length = 432

 Score =  342 bits (876), Expect = 2e-98
 Identities = 196/438 (44%), Positives = 261/438 (59%), Gaps = 40/438 (9%)

Query: 4   LVIATLALL------------GSAAANAAEADQQALVQQGEYLARAGDCVACHTAKDGKP 51
           +V+AT AL+            GSA A A  ADQ ALV++GEYLARAGDC+ACHT + GK 
Sbjct: 13  VVVATAALVPVLWSGGDNLHNGSAVA-ATPADQAALVKKGEYLARAGDCIACHTVRGGKQ 71

Query: 52  FAGGLPMETPIGVIYSTNITPD-KTGIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYA 110
           FAGGLPM TP G +++ NITPD + GIG ++ +DF +A+  G +K GS LYP  PF SY 
Sbjct: 72  FAGGLPMATPFGTMFTPNITPDDQYGIGKWTQDDFYRAMHTGRSKDGSLLYPGFPFTSYT 131

Query: 111 RVSDADMQALYAYFMKGVAPVARDNQDSDIPWPLSMRWPLSIWRWMFAPSVETPAPAAGS 170
           +V+ AD  A+YAY ++ V PV   ++  ++ +P + R  L  WR +F    E  A     
Sbjct: 132 KVTRADSDAIYAY-LRSVTPVNVASRPHELKFPFNQRNMLIGWRTLFFREGEYKA----- 185

Query: 171 DPVIS----RGAYLVEGLGHCGACHTPRALTMQEKALSASGG----SDFLSGSAPLEGWI 222
           DP  S    RGAYL+EGLGHCG CHT         +++A GG    + F  G  PL+ W 
Sbjct: 186 DPTKSVEWNRGAYLIEGLGHCGMCHT---------SINAMGGPVSSAAFAGGLIPLQNWY 236

Query: 223 AKSLRGDHKDGLGSWSEEQLVQFLKTGRSDRSAVFGGMSDVVVHSMQYMTDADLTAIARY 282
           A SL  + + GLG W  + +   LKTG S+R AVFG M++VV +S+QYMTDAD+ A+A Y
Sbjct: 237 APSLTSNKEAGLGDWETKDIADLLKTGVSNRGAVFGPMAEVVHNSLQYMTDADINAMATY 296

Query: 283 LKSLPANDPKDQPHQYDKQVAQALWNGDDSKPGAAVYIDNCAACHRTDGHGYTRVFPALA 342
           LK++P      +P Q +       + G+  K G  +Y DNCA CH  +G G    FP LA
Sbjct: 297 LKTIPQKSEAPEPLQLE---TSEKFGGELLKQGQKIYADNCAKCHADNGLGQPPAFPPLA 353

Query: 343 GNPVLQSADATSLIHIVLKGGTLPATHSAPSTFTMPAFAWRLSDQEVADVVNFIRSSWGN 402
            N  +Q   A + I +VL GG  P+T + P  + MP FA  LS+QEVA VV +IR SWGN
Sbjct: 354 NNQSIQMPSAVNPIRMVLNGGYPPSTDANPHPYGMPPFAQSLSNQEVAAVVTYIRMSWGN 413

Query: 403 QASAVKPGDVAALRNGDL 420
             +AV P  V+ LR+  L
Sbjct: 414 HGTAVSPQQVSDLRSAPL 431


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: 619
Number of extensions: 47
Number of successful extensions: 9
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: 432
Length adjustment: 32
Effective length of query: 402
Effective length of database: 400
Effective search space:   160800
Effective search space used:   160800
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