GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Leeuwenhoekiella blandensis MED217

Align Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase; D-xylose 1-dehydrogenase; D-xylose-NADP dehydrogenase; Dimeric dihydrodiol dehydrogenase; Sus2DD; EC 1.3.1.20; EC 1.1.1.179 (characterized)
to candidate WP_009779681.1 MED217_RS06420 Gfo/Idh/MocA family oxidoreductase

Query= SwissProt::Q9TV69
         (335 letters)



>NCBI__GCF_000152985.1:WP_009779681.1
          Length = 324

 Score =  180 bits (456), Expect = 5e-50
 Identities = 116/333 (34%), Positives = 177/333 (53%), Gaps = 19/333 (5%)

Query: 3   LRWGIVSAGLISSDFTTVLRLLPRSEHQVVAVAARDLSRAKEFARKHDIPKAYGSYEELA 62
           +RWGI+  G I+  F + + L+  SE  V AVA+R   +A  F   +   K Y SYE+LA
Sbjct: 4   IRWGILGLGKIAHSFASDVALVEGSE--VYAVASRSQEKADRFGATYSASKCYNSYEQLA 61

Query: 63  KDPNVEVAYIGTQHPQHKATVLLCLAAGKAVLCEKPMGVNAAEVREMVAEARSRGLFLME 122
           KDPNV+  YI T H +H    LLCL   KAVLCEKP  +N ++V EM+  A++    LME
Sbjct: 62  KDPNVDAVYIATPHVRHHQDTLLCLKHKKAVLCEKPFAMNRSQVEEMITTAQANDTLLME 121

Query: 123 AIWTRFFPAVEALRSVLAQETLGDLRVVQANFGKSIANVP--RSVDWAQAGGSLLDLGIY 180
           A+WTRF P  + ++  LA    G ++ + A+F       P  R  + A  GGSLLD+GIY
Sbjct: 122 ALWTRFMPHFKFVKEELASGRYGAVKTLTADFCFEADFNPEGRLFNKALGGGSLLDIGIY 181

Query: 181 CLQFISMVYGGQKPEKISAVGRRYETGVDDTVSVLLQYPGGVQGSFTCSITSQLSNTVSV 240
            + F ++   G KP+   A  +  +TGVD+ + +  +Y  G       SI  Q  +T ++
Sbjct: 182 PI-FCALALLG-KPDSFEAKAKIGKTGVDEEIEMTFKYNSGTTAFLNSSIVKQTPSTATL 239

Query: 241 SGTKGMAQILDPCWCPTE---LVVKGEHKEFPLPSAPGEEFNYTNGMGMCYEAKHVRECL 297
               G+  +L+  +  T+    +++G   E         +F YT G G  +E +H    L
Sbjct: 240 VCDNGIL-VLNSRFHQTDKITSILEGNKIE--------HDFAYT-GKGYYFEIEHFANLL 289

Query: 298 KKGLKESPMITLAESELLADILEEVRKAIGVTF 330
           ++  KESP+++   S  L  +L+EVR  I + +
Sbjct: 290 RENQKESPLMSFEFSRQLISMLDEVRTRIDLHY 322


Lambda     K      H
   0.319    0.134    0.397 

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: 258
Number of extensions: 8
Number of successful extensions: 5
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: 335
Length of database: 324
Length adjustment: 28
Effective length of query: 307
Effective length of database: 296
Effective search space:    90872
Effective search space used:    90872
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: 49 (23.5 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