GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Collimonas arenae Ter10

Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate WP_061534238.1 CAter10_RS16300 3-oxoacyl-ACP reductase FabG

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



>NCBI__GCF_001584165.1:WP_061534238.1
          Length = 252

 Score =  149 bits (376), Expect = 6e-41
 Identities = 96/257 (37%), Positives = 140/257 (54%), Gaps = 20/257 (7%)

Query: 2   LLKDKVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIEALG 61
           +L  KV  + GGSRGIG A+A   A +GA VA+ Y     +S G R+   ++V +IEA G
Sbjct: 9   VLAGKVAFIQGGSRGIGAAVAKRLARDGAAVALTY-----ISSGERAL--QMVKDIEAAG 61

Query: 62  RRVIAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLDMPPEVLESTVAVN 121
            R +AI+ + A  E  +  +  T+  FG++D+L +NAG+       D   E  + T+A+N
Sbjct: 62  GRALAIKADSADAEAIKAAIGQTMTKFGRLDILVNNAGVLAIAPLADFSLEDFDRTLAIN 121

Query: 122 LNGAFYVTQAAAQQMKLQGTGGAIVATSSISA----LVGGGMQTHYTPTKAGVHSLMQSC 177
           +   F  +Q AA+ M   G GG I+   S +A      GGG    Y  +K+ +  L +  
Sbjct: 122 VRSVFIASQEAARHM---GGGGRIINIGSTNADRMPFAGGG---PYAMSKSALVGLTRGL 175

Query: 178 AVALGPYGIRCNSVMPGTIATDLNAQDLADEAKKAYFEKRIPLGRLGRPEDVADCVTFLA 237
           A  LGP GI  N+V PG + TD+N    A     A  +  +P+GR G  E+VA  V +LA
Sbjct: 176 ARDLGPRGITINNVQPGPVDTDMNP---AGSDFAASLKAMMPVGRYGTAEEVAGFVAYLA 232

Query: 238 SDRARYVTGAALLVDGG 254
           S  A Y+TGA+L +DGG
Sbjct: 233 SPEAAYITGASLSIDGG 249


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: 178
Number of extensions: 10
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: 252
Length adjustment: 24
Effective length of query: 236
Effective length of database: 228
Effective search space:    53808
Effective search space used:    53808
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