GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Pseudomonas simiae WCS417

Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate GFF5024 PS417_25740 alcohol dehydrogenase

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



>FitnessBrowser__WCS417:GFF5024
          Length = 382

 Score =  254 bits (649), Expect = 3e-72
 Identities = 151/383 (39%), Positives = 220/383 (57%), Gaps = 3/383 (0%)

Query: 1   MAASTFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNI 60
           M+ S+F I    + GA ++      +        LIVTD  L K G        L ER+ 
Sbjct: 1   MSTSSFKIAHKLLTGAGAIEQLAAELTRLDVDNPLIVTDAALVKSGTVALALVHLGERSY 60

Query: 61  FSVIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDY 120
              I+D   P+P    V   +++ +E   D +I LGGGS  D AK +A  A   G + D 
Sbjct: 61  --EIFDRVLPDPEIAIVEDCMRVYREGGHDGLIGLGGGSAIDIAKSVAAYAGYHGALADL 118

Query: 121 EGVDRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLM 180
            GVD+  +   P+IAI TTAGT SE+T   I++D+A  +K  IV  ++ P +++    + 
Sbjct: 119 FGVDQVPRKGPPLIAIPTTAGTGSEVTNVAILSDKAAQLKKGIVSDYLLPDVALISPQMT 178

Query: 181 IGMPKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAR 240
           +  P+S+TAA+G+DAL HAIE+Y+S+ A+PITDA A+ A+ +IA  LP A  + +N +AR
Sbjct: 179 LTCPRSVTAASGVDALVHAIESYLSLNASPITDALAIGAIKLIAHALPKAYANPANLQAR 238

Query: 241 EAMAYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARL 300
           + MA A  +AGMAF NA +G VHA+A+ LGG +N+ HGV NA+LLP+V  +N      R+
Sbjct: 239 DDMATASLMAGMAFGNAGVGAVHALAYPLGGRFNIAHGVSNALLLPYVMHWNKLACVERM 298

Query: 301 RDCAAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALK- 359
           +D A AMGVNVTG +  + A+  + A+  L   V+IPAGL    V E+    +A  A   
Sbjct: 299 QDIAQAMGVNVTGLSVNDAADQAVEAMTRLCAAVEIPAGLHSFGVPEDAIPAMAVEAAGI 358

Query: 360 DACGFTNPIQATHEEIVAIYRAA 382
           +     NP + +  +I  IYRAA
Sbjct: 359 ERLMRNNPRKLSAADIEKIYRAA 381


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: 361
Number of extensions: 17
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: 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.

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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