GapMind for catabolism of small carbon sources

 

Alignments for a candidate for L-LDH in Methanoculleus horonobensis T10

Align L-lactate dehydrogenase; L-LDH; EC 1.1.1.27 (uncharacterized)
to candidate WP_067078821.1 MCUHO_RS09440 malate dehydrogenase

Query= curated2:B8DSV5
         (320 letters)



>NCBI__GCF_001602375.1:WP_067078821.1
          Length = 317

 Score =  171 bits (434), Expect = 2e-47
 Identities = 96/246 (39%), Positives = 145/246 (58%), Gaps = 14/246 (5%)

Query: 75  RDADMVVITAGARQKPGQSRLDLAGATINIMKSIIPNMLKVAPNAIYMLITNPVDIVTHV 134
           +D+D+++ TAG  ++PGQ R DLA     I+      + + +P+AI  L+TNPVD++T V
Sbjct: 72  KDSDVIICTAGVPRRPGQDRNDLAFENAKIIAETAETIGRTSPDAILFLVTNPVDVMTAV 131

Query: 135 AMKLSGLPASRMFGSGTNLDSARLRFLIAQQTGVNVKNVHAYIAGEHGDSEVPLWASATI 194
           A+K SG    ++FG GT+LDS RL+ LIA    V+V  VH  I GEHGDS VPLW++ TI
Sbjct: 132 ALKYSGFQPRQIFGLGTHLDSMRLKSLIAHYFRVHVSEVHTRIIGEHGDSMVPLWSATTI 191

Query: 195 GGVPMCD---WQALPGHEPLDAEARERIHQEVKNAAYKIINGKGATNYAISMSGVDIIEA 251
           GG+ + +   +  LP  E ++          V+ +   II  KG+T Y    +   ++  
Sbjct: 192 GGIRITNLPTFSGLPTQEMIET---------VRTSGEAIIRDKGSTVYGPGEAIATLVRT 242

Query: 252 ILKDSNRILPVSSLL-SDFHGISDVCMSVPTLLNRNGVNSRINTPVSDRELAALKRSAET 310
           IL D NR+L VSS + S+ HGI DVC+ VP  +NR+GV   +   + + E+A  + S + 
Sbjct: 243 ILGDENRVLTVSSYIKSEIHGIGDVCIGVPARINRDGV-FPVPLSLEEDEVAGFRESVKK 301

Query: 311 LRETAA 316
           +R+  A
Sbjct: 302 IRKVTA 307


Lambda     K      H
   0.317    0.132    0.375 

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: 249
Number of extensions: 6
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: 320
Length of database: 317
Length adjustment: 27
Effective length of query: 293
Effective length of database: 290
Effective search space:    84970
Effective search space used:    84970
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: 48 (23.1 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