GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Paucidesulfovibrio gracilis DSM 16080

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_078716111.1 B5D49_RS02645 iron-containing alcohol dehydrogenase

Query= BRENDA::P0DJA2
         (383 letters)



>NCBI__GCF_900167125.1:WP_078716111.1
          Length = 382

 Score =  261 bits (666), Expect = 3e-74
 Identities = 140/381 (36%), Positives = 226/381 (59%), Gaps = 1/381 (0%)

Query: 1   MASSTFYIPFVNEMGEGSLEKAIKDLNGSGFKNALIVSDAFMNKSGVVKQVADLLKAQGI 60
           M++  F  P     G G++ +  ++    G +  ++   +   ++G ++ V   L   G+
Sbjct: 1   MSTYIFQTPPRIIFGNGAVAQVGRETARLGSRALIVTGKSSSTRTGSLEAVTASLNEAGV 60

Query: 61  NSAVYDGVMPNPTVTAVLEGLKILKDNNSDFVISLGGGSPHDCAKAIALVATNGGEVKDY 120
           +  ++  V  +P++  V  G  + ++N  D ++ LGGGSP D AK I L+ T+ G+++DY
Sbjct: 61  HPVLFAEVESDPSIQTVEAGAALARENQCDVIVGLGGGSPLDAAKGIVLLLTHPGDIRDY 120

Query: 121 EGIDKSKKPALPLMSINTTAGTASEMTRFCIITDEVRHVKMAIVDRHVTPMVSVNDPLLM 180
                +  P +PL+SI TTAGTASE+TRF +ITD  + +KM++    + P V++ DP L 
Sbjct: 121 TS-QPADGPGMPLISIPTTAGTASEITRFTVITDTEQKIKMSLQGTALIPSVALLDPQLT 179

Query: 181 VGMPKGLTAATGMDALTHAFEAYSSTAATPITDACALKAASMIAKNLKTACDNGKDMPAR 240
           V MP+ +TAATGMDALTHA EAY S  ATP++D  AL+A  +I  NL  A D+  +M AR
Sbjct: 180 VTMPQHVTAATGMDALTHAIEAYISKLATPMSDLHALEAIRLIGANLIKAVDSPDNMAAR 239

Query: 241 EAMAYAQFLAGMAFNNASLGYVHAMAHQLGGYYNLPHGVCNAVLLPHVLAYNASVVAGRL 300
           EAM   Q  AG+AF+NAS+  VH+M+  LG  + + HG  NA+LLP V+ +N S  A R 
Sbjct: 240 EAMLRGQMHAGLAFSNASVALVHSMSRPLGALFGIAHGQANAMLLPVVMDFNRSAAADRY 299

Query: 301 KDVGVAMGLDIANLGDKEGAEATIQAVRDLAASIGIPANLTELGAKKEDVPLLADHALKD 360
           + +  A+G ++  L  ++ A+ T+ +V +L    G+  +L+  G +++D+  LA  A++ 
Sbjct: 300 RHIAEALGENVQELSARDAAKTTVLSVEELFEETGLEQHLSAYGVQEKDIARLAKDAMES 359

Query: 361 ACALTNPRQGDQKEVEELFLS 381
           A    NPR+ D + V  ++ S
Sbjct: 360 ASTAFNPRKADLESVAAIYHS 380


Lambda     K      H
   0.316    0.132    0.373 

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: 312
Number of extensions: 12
Number of successful extensions: 2
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: 383
Length of database: 382
Length adjustment: 30
Effective length of query: 353
Effective length of database: 352
Effective search space:   124256
Effective search space used:   124256
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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