GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Klebsiella michiganensis M5al

Align BadH (characterized)
to candidate BWI76_RS11090 BWI76_RS11090 beta-ketoacyl-ACP reductase

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



>FitnessBrowser__Koxy:BWI76_RS11090
          Length = 244

 Score =  168 bits (425), Expect = 1e-46
 Identities = 95/250 (38%), Positives = 140/250 (56%), Gaps = 11/250 (4%)

Query: 5   QNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRD-AGGTAEAVRCD 63
           + K A++TG   GIG A        GAK+    +    +E  A AI D  G   + +  +
Sbjct: 4   EGKIALVTGASRGIGRAIAETLVARGAKV----IGTATSESGAQAISDYLGANGKGLLLN 59

Query: 64  IADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHH 123
           + D  S+++ +       G VDILVNNAG        + +  EW  +I  NL+    +  
Sbjct: 60  VTDPASIESVLGNIRAEFGEVDILVNNAGITRDNLLMRMKDDEWNDIIETNLSSVFRLSK 119

Query: 124 AVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVV 183
           AV+  M+++RHGRI+ I S    +G++G+A YAA K GL+ FSK+LARE A  GITVNVV
Sbjct: 120 AVMRAMMKKRHGRIITIGSVVGTMGNAGQANYAAAKAGLIGFSKSLAREVASRGITVNVV 179

Query: 184 CPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQ 243
            PG  +T    D+T    + ++       A+P GRLG P+++A A+AF  SD+A +ITG+
Sbjct: 180 APGFIET----DMTRALTDEQR--AGTLAAVPAGRLGSPNEIASAVAFLASDEASYITGE 233

Query: 244 VLSVSGGLTM 253
            L V+GG+ M
Sbjct: 234 TLHVNGGMYM 243


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: 149
Number of extensions: 6
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: 244
Length adjustment: 24
Effective length of query: 231
Effective length of database: 220
Effective search space:    50820
Effective search space used:    50820
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 17 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