GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Lutibaculum baratangense AMV1

Align Alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_040486164.1 N177_RS18515 alcohol dehydrogenase AdhP

Query= reanno::Cup4G11:RR42_RS34260
         (342 letters)



>NCBI__GCF_000496075.1:WP_040486164.1
          Length = 342

 Score =  475 bits (1222), Expect = e-139
 Identities = 233/342 (68%), Positives = 272/342 (79%), Gaps = 1/342 (0%)

Query: 1   MTAMMKAAVVREFGAPLTIDEVPVPQPGRGQIQVKIEASGVCHTDLHAAEGDWPVKPTLP 60
           M  MMKAAVVRE G PL I+++ VP+ GRGQI +K+EASGVCHTDLHAA GDWPVKPT P
Sbjct: 1   MAKMMKAAVVRELGKPLVIEDMKVPEVGRGQILMKVEASGVCHTDLHAASGDWPVKPTPP 60

Query: 61  FIPGHEGVGYVSAVGAGVSRVKEGDRVGVPWLYSACGYCEHCLQGWETLCEKQQNTGYSV 120
           FIPGHEGVGYV+AVGA V+ VKEGDR+GVPWL++ACG+CEHC  GWETLC  QQ TGY+V
Sbjct: 61  FIPGHEGVGYVAAVGAEVTAVKEGDRIGVPWLHTACGHCEHCRTGWETLCYDQQMTGYTV 120

Query: 121 NGGYGEYVVADPNYVGLLPDSVGFVEIAPILCAGVTVYKGLKVTDTRPGQWVVISGIGGL 180
           NGG+ EYV+ADPNYVG LPD++ F   AP+LCAGVTVYKGLK TDT+PG WV +SGIGGL
Sbjct: 121 NGGFAEYVLADPNYVGHLPDNLDFGAAAPVLCAGVTVYKGLKETDTKPGDWVTVSGIGGL 180

Query: 181 GHVAVQYARAMGLRVAAVDIDDKKLELARKLGAEVTVNARTTDPVAFL-QKEIGGAHGAL 239
           GH+AVQYA+AMG  V AVD+ + KL+LA +LGA+ TV+AR  D V  + Q   GGAHG L
Sbjct: 181 GHMAVQYAKAMGRHVVAVDVAEDKLKLAAELGADATVDARANDAVEQVRQITDGGAHGIL 240

Query: 240 VTAVSPKAFGQAIGMVRRGGTIALNGLPPGDFPTPIFDVVLKGITIRGSIVGTRSDLQES 299
           VTAVS  AF QA+ M RRGGT+++ GLPPGDFP PIFDVVL  IT+RGSIVGTR DL E+
Sbjct: 241 VTAVSRPAFAQALAMTRRGGTMSMVGLPPGDFPLPIFDVVLNRITVRGSIVGTRQDLVEA 300

Query: 300 LDFAAHGAVKATVSTAPLEKINEIFTRMRAGDIEGRVVMDFA 341
           L FA  G V +  S   L+ IN+IF RMR G I+GRVVM  A
Sbjct: 301 LQFAGEGKVASHFSWDSLDNINDIFDRMRDGRIDGRVVMRIA 342


Lambda     K      H
   0.319    0.138    0.420 

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: 433
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: 342
Length of database: 342
Length adjustment: 29
Effective length of query: 313
Effective length of database: 313
Effective search space:    97969
Effective search space used:    97969
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 (21.7 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