GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Skermanella stibiiresistens SB22

Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_037448983.1 N825_RS07075 iron-containing alcohol dehydrogenase

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



>NCBI__GCF_000576635.1:WP_037448983.1
          Length = 387

 Score =  251 bits (642), Expect = 2e-71
 Identities = 150/381 (39%), Positives = 211/381 (55%), Gaps = 5/381 (1%)

Query: 4   STFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSV 63
           +T  +P + +IG  S+    + +A  G  R LIVTD  +   G    +   L    I   
Sbjct: 3   ATIAMPKLMLIGGGSIAQVADTLAKLGIKRPLIVTDPFMRDSGAIAKLTDPLTAAGIPFD 62

Query: 64  IYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGV 123
           ++  T P+PTTE V AG ++L +   D +I+LGGGSP D AK + ++AAN G +RDY+  
Sbjct: 63  VFADTVPDPTTEVVYAGARMLSDGGFDGMIALGGGSPIDTAKAMGVMAANPGKMRDYKVP 122

Query: 124 DRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGM 183
           +      LP++AI TTAGT SE T+F +ITD     KM I    V P  ++ D  L +  
Sbjct: 123 NPIPNESLPLLAIPTTAGTGSEATKFTVITDTETDEKMLIAGAGVIPQGAIVDFELTLSC 182

Query: 184 PKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAM 243
           P  LTA TG+D LTHAIEAYVS  A P +D+ AL A+  +A++L  A  +  N +ARE M
Sbjct: 183 PFRLTADTGIDTLTHAIEAYVSRKANPFSDSMALAAMARVAKHLRTACFEPGNREAREQM 242

Query: 244 AYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDC 303
             A   AG+AF+NAS+  VH M+  +G  +++PHG+ NA+LLP V  F+   A AR  DC
Sbjct: 243 MLAANQAGIAFSNASVALVHGMSRPIGAHFHVPHGLSNAMLLPAVTAFSLPTATARYADC 302

Query: 304 AAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACG 363
           A AMG    G +D     A ++A+  L   + +P   +   + E  F  L T   + A G
Sbjct: 303 ARAMGACAPGTDDETAGVALLDALNALNADLKVPTP-QAYGIDEGRFMGLLTLMAEQALG 361

Query: 364 F----TNPIQATHEEIVAIYR 380
                 NP   T EEIV++YR
Sbjct: 362 SGSPGNNPRVPTAEEIVSLYR 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: 389
Number of extensions: 13
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: 387
Length adjustment: 30
Effective length of query: 353
Effective length of database: 357
Effective search space:   126021
Effective search space used:   126021
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 24 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