GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdcB in Psychrobacter cryohalolentis K5

Align L-threonine dehydratase catabolic TdcB; EC 4.3.1.19; Threonine deaminase (uncharacterized)
to candidate WP_011513321.1 PCRYO_RS05055 pyridoxal-phosphate dependent enzyme

Query= curated2:Q99U50
         (346 letters)



>NCBI__GCF_000013905.1:WP_011513321.1
          Length = 326

 Score =  184 bits (467), Expect = 3e-51
 Identities = 114/320 (35%), Positives = 171/320 (53%), Gaps = 11/320 (3%)

Query: 13  IVSLGDIEEAKASIKPFIRRTPLIKSMYLSQNITKGNVYLKLENMQFTGSFKFRGASNKI 72
           I +L D+ EA   IKP+I RTP++ S +L++ +    ++ K EN Q  G+FK RGASN +
Sbjct: 10  IPTLDDMLEAHERIKPYIHRTPVLTSRFLNE-LAGCEMFFKCENFQKAGAFKVRGASNAV 68

Query: 73  NHLSDEQKAKGIIGASAGNHAQGVALTAKLLGIDATIVMPETAPIAKQNATKGYGAKVIL 132
             LSDE    G+   S+GNHA  ++  A   GI   +VMP +AP AK+ A +GYG  +  
Sbjct: 69  FGLSDEDAKNGVCTHSSGNHALSLSYAAGQRGIPCNVVMPHSAPEAKKAAVRGYGGIITE 128

Query: 133 KGKNFNETRLYMEELAKENGMTIVHPYDDKFVMAGQGTIGLEILDDIWNV----NTVIVP 188
              +         ++  E G   VHPY+D  V+AGQ T   E L+ +  +    + V+ P
Sbjct: 129 CEPSTTSREEVFAKVQAETGGDFVHPYNDPRVIAGQATCSREFLEQMEEIGEKPDMVVAP 188

Query: 189 VGGGGLIAGIATALKSFNPSIHIIGVQAENVHGMAESFYKRALTEHREDSTIADGCDVKV 248
           +GGGG+I+G    L +  P + I   +  N    A SF    +      +T+ADG  +KV
Sbjct: 189 IGGGGMISGTCLTLSNLAPDVKIYAAEPLNADDAARSFKAGHIIADDAPNTVADG--LKV 246

Query: 249 P-GEKTYEVVKHLVDEFILVSEEEIEHAMQDLMQRAKIITEGAGALPTAAILSGKIDKKW 307
           P  + T+  V + V + +  +EEEI  AM+      KII E + A+P A IL    +K  
Sbjct: 247 PLKDLTWHFVSNYVTDILTATEEEIVEAMKLTWTHMKIIIEPSCAVPLAVILK---NKDV 303

Query: 308 LEGKNVVALVSGGNVDLTRV 327
             GK V  +++GGNVDL ++
Sbjct: 304 FAGKKVGVIITGGNVDLDKL 323


Lambda     K      H
   0.315    0.133    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: 236
Number of extensions: 13
Number of successful extensions: 6
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: 346
Length of database: 326
Length adjustment: 28
Effective length of query: 318
Effective length of database: 298
Effective search space:    94764
Effective search space used:    94764
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 (21.6 bits)
S2: 49 (23.5 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