GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Pedobacter sp. GW460-11-11-14-LB5

Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate CA265_RS15450 CA265_RS15450 3-oxoacyl-[acyl-carrier-protein] reductase

Query= reanno::BFirm:BPHYT_RS16920
         (266 letters)



>FitnessBrowser__Pedo557:CA265_RS15450
          Length = 247

 Score =  129 bits (325), Expect = 5e-35
 Identities = 86/248 (34%), Positives = 125/248 (50%), Gaps = 11/248 (4%)

Query: 22  LVDRTVLITGGATGIGASFVEHFAAQGARVAFFDIDA-SAGEALADELGDSKHKPLFLSC 80
           L  +T L+TG + GIG    E FA QGA VAF  + +   GEAL  EL     K      
Sbjct: 4   LEGKTALVTGASKGIGRKIAEKFAEQGANVAFTYLSSVEKGEALEQELQSFGTKVKGYRS 63

Query: 81  DLTDIDALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVTRESFDAGIAVNIRHQFFAA 140
           D +     ++ I D+ A  G I ++VNNA   K   +  ++ E++D  I +N++  F   
Sbjct: 64  DASKFAEAEQLINDIVAEFGTIDIVVNNAGITKDGLLMRMSEENWDDVININLKSIFNVT 123

Query: 141 QAVMEDMKAANSGSIINLGSISWMLKNGGYPVYVMSKSAVQGLTRGLARDLGHFNIRVNT 200
           +A  + M  A  G  IN+GSI     NGG   Y  SK+ + G T+ +A++LG  NIR N 
Sbjct: 124 KAASKVMMKARKGVFINMGSIVGTTGNGGQANYAASKAGIIGFTKSIAKELGSRNIRANV 183

Query: 201 LVPGWVMTEKQKRLWLDDAGRRSIKEGQCIDAEL----EPADLARMALFLAADDSRMITA 256
           + PG++ TE      + D     + EG   D  L    E  D+A + +FLA+D S  +T 
Sbjct: 184 VAPGFIRTE------MTDILDPKVVEGWEKDIPLKRAGETEDIANVCVFLASDMSAYVTG 237

Query: 257 QDIVVDGG 264
           Q + V GG
Sbjct: 238 QTLSVCGG 245


Lambda     K      H
   0.320    0.134    0.388 

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: 119
Number of extensions: 5
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: 266
Length of database: 247
Length adjustment: 24
Effective length of query: 242
Effective length of database: 223
Effective search space:    53966
Effective search space used:    53966
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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