GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Echinicola vietnamensis KMM 6221, DSM 17526

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate Echvi_3364 Echvi_3364 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

Query= BRENDA::Q4J702
         (264 letters)



>FitnessBrowser__Cola:Echvi_3364
          Length = 255

 Score =  157 bits (398), Expect = 2e-43
 Identities = 87/256 (33%), Positives = 147/256 (57%), Gaps = 2/256 (0%)

Query: 1   MDIDRLFSVKGMNAVVLGASSGIGKAIAEMFSEMGGKVVLSDIDEEGLKRLSDSLRSRGH 60
           MD+  LFS+    A++ GAS GIG +IAE F+  G KVV+    +E L  ++  L  +G+
Sbjct: 1   MDLSSLFSLNNKVALITGASKGIGLSIAEFFAAAGAKVVICSRHQEHLDEIAKKLYEKGY 60

Query: 61  EVNHMKCDITDLNQVKKLVNFSLSVYGNVDALYVTPSINVRKS-IENYTYEDFEKVINVN 119
           ++  + C++   N++ +LV  ++  YG +D L      N     +   T E F+K+++VN
Sbjct: 61  DIMGIACNVGRPNELVQLVEKTIEAYGQIDILVNNAGTNPYMGPVHETTLELFDKIMDVN 120

Query: 120 LKGNFMVVKEFLSVMKNNKGGGSVVLFSSIRGTVVEPGQSVYAMTKAGIIQLAKVAAAEY 179
           +K  F + K  L  ++ +    S++  SSI     EP   +Y+++K+ +  L KV A E+
Sbjct: 121 VKAPFELSKLCLPHLRKSSQA-SIINISSIGALSPEPQLGIYSVSKSALHSLTKVCAKEW 179

Query: 180 GKYNIRVNVIAPGVVDTPLTRQIKSDPEWFKAYTEKTILKRWATPEEIANVALFLAMPAS 239
           G+  IRVN I PG++ T  ++ +  + +      ++  +KR    EEIA +ALFLA PA+
Sbjct: 180 GQQKIRVNAICPGIIKTNFSKALWGNDQIMDVIMKRLAIKRLGKTEEIAALALFLASPAA 239

Query: 240 SYITGTVIYVDGGWTA 255
           SYI+G++  VDGG+T+
Sbjct: 240 SYISGSIFTVDGGFTS 255


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: 170
Number of extensions: 11
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 17 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