GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fahA in Desulfovibrio vulgaris Hildenborough

Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate 206303 DVU0875 fumarylacetoacetate hydrolase family protein

Query= BRENDA::A0A076VF18
         (308 letters)



>MicrobesOnline__882:206303
          Length = 259

 Score =  126 bits (317), Expect = 5e-34
 Identities = 84/233 (36%), Positives = 125/233 (53%), Gaps = 21/233 (9%)

Query: 59  SPRVLTVQTLLSPLAPTDVPAIRGMGLQYSGDPAN-PQDKPPVACLFFKASQALAGPGDD 117
           +P  L+  TLL  +AP+ V  +   GL Y G       D P     F KA  A+ G G+ 
Sbjct: 33  APIPLSEITLLPVVAPSKVVCV---GLNYRGHAGELGMDVPDEPVFFLKAPTAIIGTGEP 89

Query: 118 IVLPRLARDEKNDYEVELCVVLGKDAKDVDEKDAMSFVGGYCVVNDVSSRGLCAKGGQWG 177
           IVLP      + DYE EL +V+GK  +++  + A   + G+   NDV++R +  + G +G
Sbjct: 90  IVLPPAVG--RVDYEGELALVVGKQCRNITPEQAREHIFGFTCANDVTARDIQKRDGLFG 147

Query: 178 MGKSYDTWCPFGPCLVSPSALGADPHKLTITTHVNGKLAQKGNTADLVLKIPELIARLSH 237
             K YDT+CP GP +   +AL  DP  LT+ T VNG++ Q+GNTAD+++   EL++ +S 
Sbjct: 148 RCKGYDTFCPVGPWI--ETAL-EDPGNLTLRTVVNGEVRQQGNTADMLVHPFELLSSISR 204

Query: 238 GTTLQAGSLILTGSPIALGRKAPGDAVEQSPFMKDGDEIRCFVEGCGTLINSV 290
             TL  G L+LTG+P  +G             +  GDE+R  ++  G L N V
Sbjct: 205 VMTLLPGDLVLTGTPEGIGP------------IHAGDEVRVEIDEVGLLTNPV 245


Lambda     K      H
   0.316    0.135    0.411 

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: 264
Number of extensions: 15
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: 308
Length of database: 259
Length adjustment: 26
Effective length of query: 282
Effective length of database: 233
Effective search space:    65706
Effective search space used:    65706
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: 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