GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Pseudovibrio axinellae Ad2

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_068006577.1 PsAD2_RS13045 SDR family oxidoreductase

Query= BRENDA::Q8GR61
         (262 letters)



>NCBI__GCF_001623255.1:WP_068006577.1
          Length = 263

 Score =  159 bits (403), Expect = 4e-44
 Identities = 102/269 (37%), Positives = 142/269 (52%), Gaps = 25/269 (9%)

Query: 1   MSKKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARS 60
           M  +F     L+TGAG  IG ATA+RLA+EG A+AL+D+N   LE+  AS+  +G  AR 
Sbjct: 1   MEPRFANMTALITGAGSGIGRATAIRLADEGAALALVDLNETGLEET-ASMLPEGCRARI 59

Query: 61  YVCDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGY--QGAFAPVQDYPSDDFARVLTINVT 118
           YV DV  E+AV      V   FG I  L NNAG   +G++   Q+    D+ +V  +NV 
Sbjct: 60  YVVDVADEKAVETCAVDVENTFGGISVLCNNAGMICEGSWGRSQE-DFADWRKVYEVNVL 118

Query: 119 GAFHVLKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPY 178
           GA    K    Q+     G IVNTAS+AG++      AY  SK A+I  T+T+A D   +
Sbjct: 119 GAMLFTKYTREQLKASGVGSIVNTASVAGIRAGAGGNAYSASKAALINFTKTSACDFGEH 178

Query: 179 NIRVNAISPGYMGPG-----FMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGD 233
            +RVNA+ PG +  G     F + R    + K+GS+                  +RR+GD
Sbjct: 179 GVRVNAVCPGLIETGMTKPVFDYARHAGKEEKLGSR----------------AELRRHGD 222

Query: 234 INEIPGVVAFLLGDDSSFMTGVNLPIAGG 262
             E+   +AFL   D+SF+TG  L + GG
Sbjct: 223 PTEVAATIAFLASKDASFITGQALAVDGG 251


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: 171
Number of extensions: 7
Number of successful extensions: 4
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: 263
Length adjustment: 25
Effective length of query: 237
Effective length of database: 238
Effective search space:    56406
Effective search space used:    56406
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