GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Jannaschia aquimarina GSW-M26

Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate WP_043920749.1 jaqu_RS19715 SDR family oxidoreductase

Query= metacyc::MONOMER-11802
         (255 letters)



>NCBI__GCF_000877395.1:WP_043920749.1
          Length = 250

 Score =  103 bits (257), Expect = 3e-27
 Identities = 76/243 (31%), Positives = 121/243 (49%), Gaps = 16/243 (6%)

Query: 9   IVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVEAKARELGDNARFAVADISDEQAAQS 68
           +V+GAA G+G AT +++++ G  V ++D +  A++A A  L D AR  + D+SD     +
Sbjct: 7   LVTGAARGIGLATTRLMLDRGWTVAMIDRDGPALDAAADGLRD-ARAFLCDVSDPDQVAA 65

Query: 69  AVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIGSFNLLRLAAAA 128
            +D   +AFG +  +VN AG+     + G     G  ++ +V+  NL G F + + A  A
Sbjct: 66  MIDDVRTAFGRIDAVVNNAGVA----LFGPIEETGFDTWREVMATNLDGPFLVTQAALPA 121

Query: 129 MAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAARELARFGIRVMT 188
           + E        RG ++N ASI+       + AY  SK A+  LT   A E   FGIR   
Sbjct: 122 LKES-------RGSVVNIASISGLRASTLRVAYGTSKAAVIQLTKQQAAEFGEFGIRANC 174

Query: 189 IAPGIFETPM-MAGMSDEVRASLAAGVPFPPRLGRPQEYAALARHII--ENSMLNGEVIR 245
           I PG   T + MA  + E+  +    +P   R G  +E A+    +   E S + G+V+ 
Sbjct: 175 ICPGPVRTKLAMAVHTQEIVDAYHDAIPL-NRYGSEKEIASCIAFLCSDEASYVTGQVLA 233

Query: 246 LDG 248
            DG
Sbjct: 234 ADG 236


Lambda     K      H
   0.318    0.131    0.358 

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: 105
Number of extensions: 7
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