GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tdh in Shewanella sp. ANA-3

Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 7025788 Shewana3_2938 iron-containing alcohol dehydrogenase (RefSeq)

Query= ecocyc::EG12293-MONOMER
         (383 letters)



>lcl|FitnessBrowser__ANA3:7025788 Shewana3_2938 iron-containing
           alcohol dehydrogenase (RefSeq)
          Length = 382

 Score =  520 bits (1340), Expect = e-152
 Identities = 263/381 (69%), Positives = 301/381 (79%)

Query: 3   ASTFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFS 62
           A+ FFIPSVNV+G  ++ DA+  +   GF R LIVTD  L K+G+ G+V + L +  I S
Sbjct: 2   AAKFFIPSVNVLGKGAVNDAIGDIKTLGFKRALIVTDKPLVKIGLVGEVAEKLGQNGITS 61

Query: 63  VIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEG 122
            ++DG QPNPT  NV AGL LLK N CD VISLGGGSPHDCAKGIALVA NGG I+DYEG
Sbjct: 62  TVFDGVQPNPTVGNVEAGLALLKANQCDFVISLGGGSPHDCAKGIALVATNGGSIKDYEG 121

Query: 123 VDRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIG 182
           +D+SAKPQLP++AINTTAGTASEMTRFCIITDEARHIKMAIVDKH TPLLSVND  LM+ 
Sbjct: 122 LDQSAKPQLPLVAINTTAGTASEMTRFCIITDEARHIKMAIVDKHTTPLLSVNDPELMLK 181

Query: 183 MPKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREA 242
            P SLTAATGMDALTHA+EAYVSIAA PITDACA+KA+ +I  NL  AV+ G + +ARE 
Sbjct: 182 KPASLTAATGMDALTHAVEAYVSIAANPITDACAIKAIELIQGNLVNAVKQGQDIEAREQ 241

Query: 243 MAYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRD 302
           MAYAQFLAGMAFNNASLGYVHAMAHQLGGFY+LPHGVCNA+LLPHVQ +N+KV   RL+D
Sbjct: 242 MAYAQFLAGMAFNNASLGYVHAMAHQLGGFYDLPHGVCNALLLPHVQEYNAKVVPERLKD 301

Query: 303 CAAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDAC 362
            A AMGV+V    D +GA A I AI+ L+  V+IP  L  L VK ED   LA NALKDAC
Sbjct: 302 IAKAMGVDVANMTDEQGAAAAIAAIKALSVAVNIPENLTLLGVKAEDIPTLAENALKDAC 361

Query: 363 GFTNPIQATHEEIVAIYRAAM 383
           GFTNP QATHEEI  I+  A+
Sbjct: 362 GFTNPKQATHEEICQIFANAL 382


Lambda     K      H
   0.318    0.131    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: 523
Number of extensions: 17
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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