GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Mariniradius saccharolyticus AK6

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_008628416.1 C943_RS12685 glucose 1-dehydrogenase

Query= BRENDA::Q4J702
         (264 letters)



>NCBI__GCF_000330725.2:WP_008628416.1
          Length = 255

 Score =  176 bits (447), Expect = 3e-49
 Identities = 97/255 (38%), Positives = 151/255 (59%), Gaps = 2/255 (0%)

Query: 1   MDIDRLFSVKGMNAVVLGASSGIGKAIAEMFSEMGGKVVLSDIDEEGLKRLSDSLRSRGH 60
           MD+  LFS++   A++ GAS GIG AIAE+F+  G KVV+S   +E L  ++  LR +G+
Sbjct: 1   MDLSSLFSLENKVALITGASKGIGFAIAEIFAAAGAKVVISSRKQESLDEMAAQLRQKGY 60

Query: 61  EVNHMKCDITDLNQVKKLVNFSLSVYGNVDALYVTPSIN-VRKSIENYTYEDFEKVINVN 119
           +V  + C +  ++ ++KLV+ ++  Y  +D L    + N V   + + T E F+K+I+VN
Sbjct: 61  DVTGIACHVGQMDALEKLVDATVKQYNQIDILVNNAATNPVYGPVHDTTLEAFDKIIDVN 120

Query: 120 LKGNFMVVKEFLSVMKNNKGGGSVVLFSSIRGTVVEPGQSVYAMTKAGIIQLAKVAAAEY 179
           LK  F ++      ++ + G  SV+  SSI G   EPG  +Y+++KA +I L KV A E+
Sbjct: 121 LKAPFHLMNLCFPYLRASSGA-SVINISSIGGISPEPGLGIYSVSKAALISLTKVYAKEW 179

Query: 180 GKYNIRVNVIAPGVVDTPLTRQIKSDPEWFKAYTEKTILKRWATPEEIANVALFLAMPAS 239
           G + IRVN I PG++ T     + S+ +      +   +KR   PEEI   ALFLA  AS
Sbjct: 180 GDHKIRVNAICPGLIQTKFAEALWSNEKLMHQMMKMMAIKRIGAPEEIGAAALFLASAAS 239

Query: 240 SYITGTVIYVDGGWT 254
           SY TG+++  DGG+T
Sbjct: 240 SYTTGSIVTADGGFT 254


Lambda     K      H
   0.317    0.134    0.381 

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: 163
Number of extensions: 9
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: 264
Length of database: 255
Length adjustment: 24
Effective length of query: 240
Effective length of database: 231
Effective search space:    55440
Effective search space used:    55440
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 (21.6 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