GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Paucidesulfovibrio gracilis DSM 16080

Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_078716111.1 B5D49_RS02645 iron-containing alcohol dehydrogenase

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



>NCBI__GCF_900167125.1:WP_078716111.1
          Length = 382

 Score =  268 bits (685), Expect = 2e-76
 Identities = 156/384 (40%), Positives = 225/384 (58%), Gaps = 3/384 (0%)

Query: 1   MAASTFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTD-NMLTKLGMAGDVQKALEERN 59
           M+   F  P   + G  ++       A  G +R LIVT  +  T+ G    V  +L E  
Sbjct: 1   MSTYIFQTPPRIIFGNGAVAQVGRETARLG-SRALIVTGKSSSTRTGSLEAVTASLNEAG 59

Query: 60  IFSVIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRD 119
           +  V++   + +P+ + V AG  L +EN CD ++ LGGGSP D AKGI L+  + GDIRD
Sbjct: 60  VHPVLFAEVESDPSIQTVEAGAALARENQCDVIVGLGGGSPLDAAKGIVLLLTHPGDIRD 119

Query: 120 YEGVDRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSL 179
           Y        P +P+I+I TTAGTASE+TRF +ITD  + IKM++    + P +++ D  L
Sbjct: 120 YTSQPADG-PGMPLISIPTTAGTASEITRFTVITDTEQKIKMSLQGTALIPSVALLDPQL 178

Query: 180 MIGMPKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKA 239
            + MP+ +TAATGMDALTHAIEAY+S  ATP++D  AL+A+ +I  NL  AV+   N  A
Sbjct: 179 TVTMPQHVTAATGMDALTHAIEAYISKLATPMSDLHALEAIRLIGANLIKAVDSPDNMAA 238

Query: 240 REAMAYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAAR 299
           REAM   Q  AG+AF+NAS+  VH+M+  LG  + + HG  NA+LLP V  FN   AA R
Sbjct: 239 REAMLRGQMHAGLAFSNASVALVHSMSRPLGALFGIAHGQANAMLLPVVMDFNRSAAADR 298

Query: 300 LRDCAAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALK 359
            R  A A+G NV   +  + A+  + ++ EL ++  +   L    V+E+D A LA +A++
Sbjct: 299 YRHIAEALGENVQELSARDAAKTTVLSVEELFEETGLEQHLSAYGVQEKDIARLAKDAME 358

Query: 360 DACGFTNPIQATHEEIVAIYRAAM 383
            A    NP +A  E + AIY + +
Sbjct: 359 SASTAFNPRKADLESVAAIYHSLL 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: 325
Number of extensions: 12
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: 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 Apr 09 2024. 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