GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Gallaecimonas xiamenensis 3-C-1

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_008486155.1 B3C1_RS16220 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD

Query= metacyc::MONOMER-16231
         (254 letters)



>NCBI__GCF_000299915.1:WP_008486155.1
          Length = 249

 Score =  161 bits (407), Expect = 1e-44
 Identities = 99/248 (39%), Positives = 141/248 (56%), Gaps = 3/248 (1%)

Query: 1   MKLLEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIA 60
           M  L GK  LVTGAS G+G+A A+G A++GA+V I  +  +G     VA+I ALG +A A
Sbjct: 1   MFALNGKRALVTGASRGLGQAMALGLAENGAEV-ICASSREGGCDDTVAKILALGGKARA 59

Query: 61  VKGDVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAY 120
           +  D+ D Q  Q    +A+   G VDV+V+N G     A LD P+D  +   KVNL+ A+
Sbjct: 60  LAADLGDSQAVQALAEQALAA-GPVDVLVNNGGCIYREAALDFPLDAFDAVIKVNLNAAF 118

Query: 121 FMVQAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGI 180
            + Q   + MV +G  G IV ++S+ +  GG     YT +K  +  L ++ A   G+HGI
Sbjct: 119 QLSQLLGRAMVTKG-SGKIVNIASMLSYSGGIRVPAYTASKHAIAGLTKALANEWGQHGI 177

Query: 181 RCNSVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTG 240
           + N++ PG   T+  +    D E+   +E R P GR G P+DL G +VFLAS  + YV G
Sbjct: 178 QVNAIAPGYFRTDNTQALQDDAERSSEIEKRIPAGRWGNPDDLKGAVVFLASKASDYVNG 237

Query: 241 AALLVDGG 248
             L VDGG
Sbjct: 238 HILAVDGG 245


Lambda     K      H
   0.318    0.133    0.379 

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: 132
Number of extensions: 8
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: 254
Length of database: 249
Length adjustment: 24
Effective length of query: 230
Effective length of database: 225
Effective search space:    51750
Effective search space used:    51750
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 (21.7 bits)
S2: 46 (22.3 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