GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Novosphingobium barchaimii LL02

Align BadH (characterized)
to candidate WP_059149763.1 V474_RS01280 SDR family oxidoreductase

Query= metacyc::MONOMER-893
         (255 letters)



>NCBI__GCF_001046635.1:WP_059149763.1
          Length = 250

 Score =  181 bits (459), Expect = 1e-50
 Identities = 101/250 (40%), Positives = 144/250 (57%), Gaps = 7/250 (2%)

Query: 4   LQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCD 63
           L  K AVITG G GIG     R A++ A IAV+DLN + A +    I  AGG A A+  D
Sbjct: 5   LDGKVAVITGAGSGIGRGIALRLAEDKAAIAVWDLNPEGAAETVKLIEAAGGKALAIVAD 64

Query: 64  IADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHH 123
            +D+ ++ AA   T    GP+ ILVNNAG   F PF      E++++I INL G   +  
Sbjct: 65  CSDKAAIRAAADETRAKFGPITILVNNAGIAPFTPFMDIPEDEFDKVIRINLKGPWLVTR 124

Query: 124 AVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVV 183
            ++P M+  + GRI+NI S + + GS  ++ Y A KGGL+  +K LA E  + GIT N++
Sbjct: 125 EIVPDMLAAQWGRIINITSSSTQSGSFAQSHYVASKGGLLGLTKALALELGKTGITANMI 184

Query: 184 CPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQ 243
            PG  DT +L      A       EA+  ++P+GRLG+  D+A A AF  S++A ++TGQ
Sbjct: 185 PPGSIDTPMLRSAPIDA-------EAYGASLPVGRLGQVADIAAAAAFLASEEASYMTGQ 237

Query: 244 VLSVSGGLTM 253
            +S +GG  M
Sbjct: 238 TISTNGGRYM 247


Lambda     K      H
   0.318    0.135    0.398 

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: 175
Number of extensions: 8
Number of successful extensions: 2
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: 255
Length of database: 250
Length adjustment: 24
Effective length of query: 231
Effective length of database: 226
Effective search space:    52206
Effective search space used:    52206
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