GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Klebsiella michiganensis M5al

Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate BWI76_RS22480 BWI76_RS22480 lactaldehyde reductase

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



>FitnessBrowser__Koxy:BWI76_RS22480
          Length = 383

 Score =  276 bits (707), Expect = 5e-79
 Identities = 155/381 (40%), Positives = 218/381 (57%), Gaps = 5/381 (1%)

Query: 3   ASTFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFS 62
           A    +   +  G  S++  ++ +   GF + L+VTD  L +  +A  V   L+   +  
Sbjct: 2   AYRMILNETSYFGPGSISCIVDEVKKRGFKKALVVTDKDLIRFNVATKVLAILDGAGLPY 61

Query: 63  VIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANG--GDIRDY 120
            I+D   PNPT E V  G++  K++  D +I++GGGSP D  K I ++  N    D+R  
Sbjct: 62  SIFDDVVPNPTIEVVQQGVETFKQSGADYLIAIGGGSPQDTCKAIGIIINNPEFADVRSL 121

Query: 121 EGVDRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLM 180
           EG   +    +PMIAI TTAGTA+E+T   +ITD     K    D H  PL+++ D+ +M
Sbjct: 122 EGGADTKNAAVPMIAIPTTAGTAAEVTINYVITDVQNRRKFVCYDPHDIPLVAIIDAEMM 181

Query: 181 IGMPKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAR 240
             MP SL AATG+DALTHAIE Y++  A  +TD   LKA+ +I  +L  +V+   +A+  
Sbjct: 182 ASMPASLKAATGVDALTHAIEGYITKGAWELTDMLHLKAIEVIGRSLRASVQ--GDAQGA 239

Query: 241 EAMAYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARL 300
           E MA  Q++AGM F+N  LG VH MAH LG FY  PHGV NAVLLPH+  +N++    + 
Sbjct: 240 EGMALGQYIAGMGFSNVGLGLVHGMAHPLGAFYGTPHGVANAVLLPHIMAYNAEYTGEKY 299

Query: 301 RDCAAAMG-VNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALK 359
           RD A A+G  +      AE  +A I A+ +L + V+IPA LRD+ +KEED   LA  AL 
Sbjct: 300 RDIAVALGNKSAATMPIAEARQAAIEAVAQLNRDVNIPARLRDVGMKEEDIDALAAAALA 359

Query: 360 DACGFTNPIQATHEEIVAIYR 380
           D C   NP     EEI  +YR
Sbjct: 360 DVCTGGNPRDTNLEEIKTLYR 380


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: 410
Number of extensions: 20
Number of successful extensions: 4
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: 383
Length adjustment: 30
Effective length of query: 353
Effective length of database: 353
Effective search space:   124609
Effective search space used:   124609
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