GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Shewanella sp. ANA-3

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate 7025788 Shewana3_2938 iron-containing alcohol dehydrogenase (RefSeq)

Query= BRENDA::P0DJA2
         (383 letters)



>FitnessBrowser__ANA3:7025788
          Length = 382

 Score =  497 bits (1279), Expect = e-145
 Identities = 246/380 (64%), Positives = 298/380 (78%)

Query: 3   SSTFYIPFVNEMGEGSLEKAIKDLNGSGFKNALIVSDAFMNKSGVVKQVADLLKAQGINS 62
           ++ F+IP VN +G+G++  AI D+   GFK ALIV+D  + K G+V +VA+ L   GI S
Sbjct: 2   AAKFFIPSVNVLGKGAVNDAIGDIKTLGFKRALIVTDKPLVKIGLVGEVAEKLGQNGITS 61

Query: 63  AVYDGVMPNPTVTAVLEGLKILKDNNSDFVISLGGGSPHDCAKAIALVATNGGEVKDYEG 122
            V+DGV PNPTV  V  GL +LK N  DFVISLGGGSPHDCAK IALVATNGG +KDYEG
Sbjct: 62  TVFDGVQPNPTVGNVEAGLALLKANQCDFVISLGGGSPHDCAKGIALVATNGGSIKDYEG 121

Query: 123 IDKSKKPALPLMSINTTAGTASEMTRFCIITDEVRHVKMAIVDRHVTPMVSVNDPLLMVG 182
           +D+S KP LPL++INTTAGTASEMTRFCIITDE RH+KMAIVD+H TP++SVNDP LM+ 
Sbjct: 122 LDQSAKPQLPLVAINTTAGTASEMTRFCIITDEARHIKMAIVDKHTTPLLSVNDPELMLK 181

Query: 183 MPKGLTAATGMDALTHAFEAYSSTAATPITDACALKAASMIAKNLKTACDNGKDMPAREA 242
            P  LTAATGMDALTHA EAY S AA PITDACA+KA  +I  NL  A   G+D+ ARE 
Sbjct: 182 KPASLTAATGMDALTHAVEAYVSIAANPITDACAIKAIELIQGNLVNAVKQGQDIEAREQ 241

Query: 243 MAYAQFLAGMAFNNASLGYVHAMAHQLGGYYNLPHGVCNAVLLPHVLAYNASVVAGRLKD 302
           MAYAQFLAGMAFNNASLGYVHAMAHQLGG+Y+LPHGVCNA+LLPHV  YNA VV  RLKD
Sbjct: 242 MAYAQFLAGMAFNNASLGYVHAMAHQLGGFYDLPHGVCNALLLPHVQEYNAKVVPERLKD 301

Query: 303 VGVAMGLDIANLGDKEGAEATIQAVRDLAASIGIPANLTELGAKKEDVPLLADHALKDAC 362
           +  AMG+D+AN+ D++GA A I A++ L+ ++ IP NLT LG K ED+P LA++ALKDAC
Sbjct: 302 IAKAMGVDVANMTDEQGAAAAIAAIKALSVAVNIPENLTLLGVKAEDIPTLAENALKDAC 361

Query: 363 ALTNPRQGDQKEVEELFLSA 382
             TNP+Q   +E+ ++F +A
Sbjct: 362 GFTNPKQATHEEICQIFANA 381


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: 495
Number of extensions: 23
Number of successful extensions: 1
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 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