GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Halococcus hamelinensis 100A6

Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate WP_007690492.1 C447_RS02270 SDR family oxidoreductase

Query= reanno::BFirm:BPHYT_RS28235
         (260 letters)



>NCBI__GCF_000336675.1:WP_007690492.1
          Length = 256

 Score =  158 bits (400), Expect = 9e-44
 Identities = 102/256 (39%), Positives = 149/256 (58%), Gaps = 14/256 (5%)

Query: 2   LLKDKVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAE-IEAL 60
           +++++  IVTG SRGIG+ +A   AA+GA+V +           R    +E VAE IEA 
Sbjct: 1   MVENETAIVTGSSRGIGKQVAKTLAADGANVVV---------CSRSVEDSEAVAEGIEAD 51

Query: 61  GRRVIAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLDMPPEVLESTVAV 120
           G   +A+E +V+ +E+ ++LV  TVEAFG+VD L +NAGI       +M PE  +  + V
Sbjct: 52  GGSALAVEVDVSEKESVERLVERTVEAFGRVDTLVNNAGINIRGPAEEMAPEDWQKVMDV 111

Query: 121 NLNGAFYVTQAAAQQMKLQGTGGAIVATSSISALVGGGMQTHYTPTKAGVHSLMQSCAVA 180
           NL G FY  QA  +++  QG GG IV  SS+   +G   +T Y  +K G+++L +  AV 
Sbjct: 112 NLTGPFYCAQAVGKRLIEQGDGGDIVNISSMMGEMGQQDRTPYNTSKGGINNLTRCLAVE 171

Query: 181 LGPYGIRCNSVMPGTIATDL--NAQDLADEAKKAYFEKRIPLGRLGRPEDVADCVTFLAS 238
              + I  N++ PG I TD+   AQ+ AD  ++     R PL R G PE++A+CV+FLAS
Sbjct: 172 WAEHDIYVNALAPGYIMTDMAAEAQEEADFTEQD-VRDRTPLDRFGTPEEIANCVSFLAS 230

Query: 239 DRARYVTGAALLVDGG 254
               Y+TG  L  DGG
Sbjct: 231 -HDHYMTGEVLHADGG 245


Lambda     K      H
   0.319    0.134    0.386 

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: 174
Number of extensions: 12
Number of successful extensions: 3
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: 260
Length of database: 256
Length adjustment: 24
Effective length of query: 236
Effective length of database: 232
Effective search space:    54752
Effective search space used:    54752
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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