GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Methanobacterium veterum MK4

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_048081445.1 EJ01_RS05790 3-oxoacyl-ACP reductase FabG

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



>NCBI__GCF_000745485.1:WP_048081445.1
          Length = 258

 Score =  144 bits (362), Expect = 2e-39
 Identities = 88/255 (34%), Positives = 144/255 (56%), Gaps = 11/255 (4%)

Query: 4   LEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKG 63
           L+GK  +VTGAS G+G  AA   AQ GADVA+  A      +S   EIE+ G +A+AV+ 
Sbjct: 7   LKGKVAVVTGASGGLGADAARAYAQEGADVAL-LARRKERLESLAEEIESAGVKALAVQC 65

Query: 64  DVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFMV 123
           DVAD ++ ++ + + ++ FGK+D++++NAGI        + V+  ++   VN+ G + + 
Sbjct: 66  DVADEESVENAIDEVIKYFGKIDILLNNAGIAVRGGVHSLSVEDWDKGMDVNVKGIFLVS 125

Query: 124 QAAAQQMVRQGHGGSIVAVSSISALVGGEYQTH----YTPTKAGVHSLMQSTAIALGKHG 179
           +     M++  + G IV  SSI+++ G + +      Y  +KA V  L    A + GK+G
Sbjct: 126 KYVLPHMMKNNY-GKIVNTSSINSIAGDKSEMFIRHVYNASKAAVRGLTMGMACSYGKYG 184

Query: 180 IRCNSVLPGTILTEINKDDLADQEKREYMEART---PLGRLGAPEDLAGPIVFLASDMAA 236
           I  N+V P    +E+  + L   E  E++E  +   PL R     +L GPI+FL+S+ ++
Sbjct: 185 ITVNAVAPALFESEMTSNTLFKSE--EFLERYSNVVPLNRPAKKGELNGPIIFLSSEASS 242

Query: 237 YVTGAALLVDGGMYV 251
           Y+TG  + VDGG  V
Sbjct: 243 YITGQTIFVDGGFSV 257


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: 119
Number of extensions: 5
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: 258
Length adjustment: 24
Effective length of query: 230
Effective length of database: 234
Effective search space:    53820
Effective search space used:    53820
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: 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