GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Herbaspirillum seropedicae SmR1

Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate HSERO_RS16735 HSERO_RS16735 alcohol dehydrogenase

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



>FitnessBrowser__HerbieS:HSERO_RS16735
          Length = 444

 Score =  488 bits (1257), Expect = e-142
 Identities = 251/417 (60%), Positives = 306/417 (73%), Gaps = 8/417 (1%)

Query: 3   ALVIATLALLGSAAANAA--EADQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMET 60
           A V++  AL  +A +N A   ADQQ LVQ+GEYLA+AGDCVACHTAK GKPFAGGL + T
Sbjct: 14  AAVMSLSALTAAAQSNPAAPSADQQ-LVQRGEYLAKAGDCVACHTAKGGKPFAGGLAIAT 72

Query: 61  PIGVIYSTNITPDK-TGIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQA 119
           PIG +YS+NITPDK  GIG+YS EDFD+A+RHG+ K G++LYPAMP+PSYA+V  AD++A
Sbjct: 73  PIGTVYSSNITPDKENGIGNYSEEDFDRALRHGIRKDGASLYPAMPYPSYAKVKPADVKA 132

Query: 120 LYAYFMKGVAPVARDNQDSDIPWPLSMRWPLSIWRWMFAPSVETPAPAAGSDPVISRGAY 179
           LYAYFM GV      N+  DI WPLSMRWPLSIWR +FAP+V    P   S  V  RG Y
Sbjct: 133 LYAYFMHGVQADPAPNRGVDITWPLSMRWPLSIWRKVFAPAVAVDGPEDNSPLV--RGQY 190

Query: 180 LVEGLGHCGACHTPRALTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSE 239
           LVEGLGHCGACHTPR + MQEKALS +  S FLSG   ++G++A +LRGD +DGLG+WSE
Sbjct: 191 LVEGLGHCGACHTPRGVGMQEKALS-NDSSQFLSGGV-IDGYLANNLRGDGRDGLGNWSE 248

Query: 240 EQLVQFLKTGRSDRSAVFGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKDQPHQYD 299
             +V FLKTGR+  SA FGGM+DVV +S QYMT+ DL+A+A+YLKSL           YD
Sbjct: 249 ADIVAFLKTGRNSHSAAFGGMADVVANSTQYMTEEDLSAMAKYLKSLKPVKDGTPALAYD 308

Query: 300 KQVAQALWNGDDSKPGAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSADATSLIHIV 359
            +  QAL  G D  PGA  +++NCAACHR+ G GY   FP+LA +P + + +  SLI IV
Sbjct: 309 DKTHQALRKGSDQSPGAMAFLNNCAACHRSSGKGYDETFPSLALSPTVNAENPASLIRIV 368

Query: 360 LKGGTLPATHSAPSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGDVAALR 416
           L+G  +P TH AP+ F MPAF  RLSDQEVA+VV FIRSSWGNQAS+V   DVA +R
Sbjct: 369 LEGAEMPWTHKAPTQFAMPAFGSRLSDQEVAEVVTFIRSSWGNQASSVSASDVAKVR 425


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: 679
Number of extensions: 45
Number of successful extensions: 7
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: 444
Length adjustment: 32
Effective length of query: 402
Effective length of database: 412
Effective search space:   165624
Effective search space used:   165624
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