GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Bacteroides clarus YIT 12056

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_009122055.1 BUB52_RS10260 gluconate 5-dehydrogenase

Query= reanno::ANA3:7024897
         (256 letters)



>NCBI__GCF_900129655.1:WP_009122055.1
          Length = 267

 Score =  119 bits (299), Expect = 5e-32
 Identities = 78/258 (30%), Positives = 136/258 (52%), Gaps = 10/258 (3%)

Query: 5   NQYP--SLQGKTIFISGGATGIGACLVNAFLEQGAKVAFVDILVEESTQLVADLKQTQPE 62
           NQY   SL+GK   ++G + GIG  + +AF EQGAK+ F DI  E   + +A   +   +
Sbjct: 2   NQYLNFSLEGKVALVTGASYGIGFAIASAFAEQGAKICFNDINQELVDKGIAAYAEKGIQ 61

Query: 63  ASVTFYHCDLVDIAALKRVIAQVEDDLGPISVLINNAACDQRHSIDEVTPEYWDQCLNTN 122
           A    Y CD+ D  A++ ++A +E ++G + +L+NNA   +R  + E+    + + ++ +
Sbjct: 62  AHG--YVCDVTDEPAVQAMVATIEKEVGSVDILVNNAGIIRRIPMHEMEAADFRKVIDID 119

Query: 123 LRHYFFAVQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLG 182
           L   F   +AV P M + G G +IN+ SM     +  ++ Y A+K G   LTR + ++ G
Sbjct: 120 LNAPFIVSKAVLPAMMKKGHGKIINICSMMSELGRETVSAYAAAKGGLKMLTRNICSEYG 179

Query: 183 KDKIRINTLTPGWVMTKRQL-THWVDKDTAKH-IENNQCIK----EYVMPEDIAAMALFL 236
           +  I+ N + PG++ T +         D ++H  ++  C K     ++ PE++   A+FL
Sbjct: 180 EYNIQCNGIGPGYIATPQTAPLREKQADGSRHPFDSFICAKTPAGRWLDPEELTGPAVFL 239

Query: 237 AADDSKLCTAQNFIVDGG 254
           A++ S         VDGG
Sbjct: 240 ASEASNAVNGHILYVDGG 257


Lambda     K      H
   0.320    0.134    0.406 

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: 153
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: 256
Length of database: 267
Length adjustment: 25
Effective length of query: 231
Effective length of database: 242
Effective search space:    55902
Effective search space used:    55902
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 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