GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Desulfovibrio vulgaris Hildenborough

Align Short-chain alcohol dehydrogenase protein (characterized, see rationale)
to candidate 206645 3-oxoacyl-(acyl-carrier-protein) reductase

Query= uniprot:D8IS13
         (254 letters)



>MicrobesOnline__882:206645
          Length = 259

 Score =  120 bits (302), Expect = 2e-32
 Identities = 82/250 (32%), Positives = 127/250 (50%), Gaps = 22/250 (8%)

Query: 12  TVLITAAAQGIGRASTELFAREGARVIATDISKPHLDEL--AGI----AGVETHLLDVTD 65
           T ++T  ++GIG+A  E  AR G +V  T +SKP   E   AGI           LDV+D
Sbjct: 19  TAIVTGGSRGIGKAVAETLARAGLQVFLTYVSKPDEAEAVAAGIRDAGGSATAFRLDVSD 78

Query: 66  DAAIKAL----VAKIGTIDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAVL 121
            AA+ A     +     +DVL N AG    G I+   D+ ++   ++N    F  +R   
Sbjct: 79  AAAVAAFFQSEIKDKVRLDVLVNNAGITKDGLIMRMKDEDFERVLDVNLCGAFTCLREAS 138

Query: 122 PGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVAQGIRCNAICP 181
             M  ++ G I+NI S    + G A +  Y A+KA ++GLTKS A +  A+ +  NA+ P
Sbjct: 139 KLMTRQRLGRIINITSVVGQM-GNAGQANYCAAKAGLIGLTKSAAKELAARNVTVNAVAP 197

Query: 182 GTIESPSLNQRISTQAKETGKSEEEVRAAFVGRQPMGRIGKAEEVAALALYLASDESNFT 241
           G IE+             T    EEVR A+V   P+ R+G A+++A    +LAS+ +++ 
Sbjct: 198 GFIETDM-----------TAGLPEEVRKAYVEAIPLRRLGSAQDIADAVAFLASERASYI 246

Query: 242 TGSIHMIDGG 251
           TG +  ++GG
Sbjct: 247 TGQVLAVNGG 256


Lambda     K      H
   0.317    0.130    0.365 

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: 136
Number of extensions: 8
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: 254
Length of database: 259
Length adjustment: 24
Effective length of query: 230
Effective length of database: 235
Effective search space:    54050
Effective search space used:    54050
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: 47 (22.7 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