GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Burkholderia phytofirmans PsJN

Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate BPHYT_RS31860 BPHYT_RS31860 alcohol dehydrogenase

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



>FitnessBrowser__BFirm:BPHYT_RS31860
          Length = 393

 Score =  197 bits (500), Expect = 6e-55
 Identities = 127/386 (32%), Positives = 196/386 (50%), Gaps = 10/386 (2%)

Query: 3   ASTFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFS 62
           A+  + P +  IG  ++     +   +G +  LIVTD  + K  +   +   L   +I  
Sbjct: 4   AALLYSPRLLDIGGGAVRRTAALCRRFGISHPLIVTDPYMIKSKLICVLTDTLSAASIEF 63

Query: 63  VIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVA-----ANGGDI 117
            I+  T  +PT E V  G++LL   N D+VI+ GGGSP D AK I ++A          +
Sbjct: 64  AIFSDTVADPTDEVVDVGVELLNSGNFDAVIAFGGGSPIDTAKAINILAHARRTEPSACM 123

Query: 118 RDYEGVDRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDS 177
           RDY+  + +    LP+IAI TTAGT SE+TRF +ITD     KM I      P+ ++ D 
Sbjct: 124 RDYKMPELADHAALPLIAIPTTAGTGSEVTRFTVITDIGLDEKMLISGLGALPIAAIVDY 183

Query: 178 SLMIGMPKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNA 237
            L + MP  LTA TG+D+ THA+EA+VS  A   +D  A  A+++I  +L  A  +  N 
Sbjct: 184 QLTLDMPPRLTADTGIDSFTHALEAFVSRHANANSDLFARSALSLIGTHLKTAYTEPHNH 243

Query: 238 KAREAMAYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAA 297
            AREAM      AG+A + A +  VH MA  +G  +++PHG+ NA++LP V  ++ + A 
Sbjct: 244 AAREAMMLGATHAGIACSIAPVALVHGMARPIGAHFHVPHGLSNAMMLPAVTAYSLRSAL 303

Query: 298 ARLRDCAAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDF----AVL 353
            R  + A   G      ND E     +  +RE+ + + +P+  R   +  + +     ++
Sbjct: 304 PRYAEVARLAGFATASDNDEEAGLKLVEGLREMNRDLTVPSP-RAYGINPDGWHAKKTLM 362

Query: 354 ATNALKDACGFTNPIQATHEEIVAIY 379
           A  AL       NP   T  +I  +Y
Sbjct: 363 AEQALASGSPANNPKVPTKADIETLY 388


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: 370
Number of extensions: 17
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: 393
Length adjustment: 30
Effective length of query: 353
Effective length of database: 363
Effective search space:   128139
Effective search space used:   128139
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