GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Escherichia coli BW25113

Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 16552 b2453 ethanolamine utilization; homolog of Salmonella enzyme, similar to iron-containing alcohol dehydrogenase (VIMSS)

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



>FitnessBrowser__Keio:16552
          Length = 395

 Score =  240 bits (613), Expect = 4e-68
 Identities = 140/378 (37%), Positives = 202/378 (53%), Gaps = 6/378 (1%)

Query: 5   TFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVI 64
           TF +P V + G  S++         G     ++ D+ L + GM   + ++L  + I   +
Sbjct: 23  TFSVPPVTLCGPGSVSSCGQQAQTRGLKHLFVMADSFLHQAGMTAGLTRSLTVKGIAMTL 82

Query: 65  YDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVD 124
           +      P   +V A +  L+E+ CD VI+ GGGS  D AK + L+  N           
Sbjct: 83  WPCPVGEPCITDVCAAVAQLRESGCDGVIAFGGGSVLDAAKAVTLLVTNPDSTLAEMSET 142

Query: 125 RSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMP 184
              +P+LP+IAI TTAGT SE T   +I D     K  +    + P +++ D++L  G+P
Sbjct: 143 SVLQPRLPLIAIPTTAGTGSETTNVTVIIDAVSGRKQVLAHASLMPDVAILDAALTEGVP 202

Query: 185 KSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMA 244
             +TA TG+DALTHAIEAY ++ ATP TD+ A+ A+ MI ++LP AV  G +  ARE+M 
Sbjct: 203 SHVTAMTGIDALTHAIEAYSALNATPFTDSLAIGAIAMIGKSLPKAVGYGHDLAARESML 262

Query: 245 YAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCA 304
            A  +AGMAF++A LG  HAMAHQ G   ++PHG+ NA+LLP V  FN  V   R     
Sbjct: 263 LASCMAGMAFSSAGLGLCHAMAHQPGAALHIPHGLANAMLLPTVMEFNRMVCRERFSQIG 322

Query: 305 AAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACGF 364
            A+    +   DA      INA+ EL  +V I   L D+      +   A  AL+D C  
Sbjct: 323 RALRTKKSDDRDA------INAVSELIAEVGIGKRLGDVGATSAHYGAWAQAALEDICLR 376

Query: 365 TNPIQATHEEIVAIYRAA 382
           +NP  A+ E+IV +Y AA
Sbjct: 377 SNPRTASLEQIVGLYAAA 394


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: 368
Number of extensions: 21
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: 395
Length adjustment: 30
Effective length of query: 353
Effective length of database: 365
Effective search space:   128845
Effective search space used:   128845
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