GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Phyllobacterium brassicacearum STM 196

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_106712313.1 CU102_RS17075 L-iditol 2-dehydrogenase

Query= BRENDA::Q8GR61
         (262 letters)



>NCBI__GCF_003010955.1:WP_106712313.1
          Length = 258

 Score =  130 bits (327), Expect = 3e-35
 Identities = 84/262 (32%), Positives = 137/262 (52%), Gaps = 13/262 (4%)

Query: 4   KFNGKVCLVTGAGGNIGLATALRLAEEGTA-IALLDMNREALEKAEASVREKGVEARSYV 62
           +  GK   +TG+   IG A A     E  A + + D+N   LE+A+ + RE G  A +  
Sbjct: 3   RLEGKTAFITGSARGIGRAFAEAYLRESAAHVVIADIN---LERAQETARELGAGAYAVR 59

Query: 63  CDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFH 122
            DVT + ++   V   V  FG ID L NNA      AP+ +   + + ++  +N +G   
Sbjct: 60  LDVTDQASIDAAVSETVTKFGGIDVLINNAALFD-LAPIVEITRESYEKLFAVNFSGTLF 118

Query: 123 VLKAVSRQMITQNYG-RIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIR 181
            L+AV++ MI +  G +I+N AS AG +G P +A Y  +K A+I+LT++A L+L  + I 
Sbjct: 119 TLQAVAKAMIARGKGGKIINMASQAGRRGEPLVAIYCATKAAVISLTQSAGLNLIEHGIN 178

Query: 182 VNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIG-SVPMRRYGDINEIPGV 240
           VNA++PG +  G  WE    L AK     +   P+   ++++G +VP  R G   ++ G+
Sbjct: 179 VNAMAPGVV-DGEHWEGVDALFAK-----YENRPRGEKKRLVGEAVPYGRMGTAEDLTGM 232

Query: 241 VAFLLGDDSSFMTGVNLPIAGG 262
             FL   +S ++      + GG
Sbjct: 233 AIFLASSESDYIVAQTYNVDGG 254


Lambda     K      H
   0.318    0.135    0.384 

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: 159
Number of extensions: 12
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: 262
Length of database: 258
Length adjustment: 24
Effective length of query: 238
Effective length of database: 234
Effective search space:    55692
Effective search space used:    55692
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 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