GapMind for catabolism of small carbon sources

 

Alignments for a candidate for x5p-reductase in Rhodococcus qingshengii djl-6-2

Align Lmo2663 protein (characterized, see rationale)
to candidate WP_042452947.1 C1M55_RS07990 NAD(P)-dependent alcohol dehydrogenase

Query= uniprot:Q8Y414
         (343 letters)



>NCBI__GCF_002893965.1:WP_042452947.1
          Length = 346

 Score = 99.8 bits (247), Expect = 9e-26
 Identities = 69/210 (32%), Positives = 100/210 (47%), Gaps = 20/210 (9%)

Query: 14  MELKDVEEPQVYGDKVKIKVAFTGICGSDIHTFKGEYKNPTTPVTLGHEFSGVVVEVGPD 73
           +E   VE  ++    + I + F GIC SDIHT + E+     P+  GHE +GVV  VG D
Sbjct: 16  LEKTTVERRELGPLDILIDIKFAGICHSDIHTARNEWGGAKYPIVPGHEIAGVVAAVGSD 75

Query: 74  VTSIKVGDRVTSETTFETCGECIYCKEHDYNLCSNRRGI----------GTQANGSFAEF 123
           VT  KVGDRV      ++CGEC  C   +   C  R+G+          G +  G ++  
Sbjct: 76  VTKHKVGDRVGVGCFVDSCGECDACTAGEEQYC--RKGVTGTYNATGRDGERTQGGYSTH 133

Query: 124 VLSREESCHVLDERISLEAAALTEPLACC---VHSALEKTTIRPDDTVLVFGPGPIGLLL 180
           ++  E     + E I L+ AA   PL C    ++S L      P   V + G G +G + 
Sbjct: 134 IVVTEHFVLSIPEGIELDVAA---PLLCAGITLYSPLRHWNAGPGKKVAIIGFGGLGHVG 190

Query: 181 AQVVKAQGA--TVIMAGITKDSDRLRLAKE 208
            ++ KA GA  TV+   + K  D LRL  +
Sbjct: 191 VKIAKALGAEVTVLSQTLGKKEDGLRLGAD 220


Lambda     K      H
   0.317    0.135    0.392 

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: 297
Number of extensions: 21
Number of successful extensions: 1
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: 343
Length of database: 346
Length adjustment: 29
Effective length of query: 314
Effective length of database: 317
Effective search space:    99538
Effective search space used:    99538
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 (21.6 bits)
S2: 49 (23.5 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