GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdcB in Sphingobium czechense LL01

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_066603969.1 V473_RS11265 threonine/serine dehydratase

Query= BRENDA::Q74FW6
         (402 letters)



>NCBI__GCF_001046645.1:WP_066603969.1
          Length = 330

 Score =  196 bits (497), Expect = 1e-54
 Identities = 115/301 (38%), Positives = 162/301 (53%), Gaps = 5/301 (1%)

Query: 20  RTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREALAKGVITASAGNH 79
           RT L+ +H  +++LG  +  K E  Q TG+FK RGA N +     +  A GV+  S+GNH
Sbjct: 25  RTPLLENHALNDRLGRRVLIKFEGAQHTGSFKFRGAYNRLARLDAQQRAAGVVAWSSGNH 84

Query: 80  AQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDEAYAAAVQAQEERG 139
           AQGVA +A LL +P+T+ MP   P  K+   R  GAE+V   R+ +     A      RG
Sbjct: 85  AQGVAAAAQLLALPATIVMPSDAPAIKLANNRALGAEIVTYDRHSESREEIATALAHSRG 144

Query: 140 ALFVHPFDDPLVMAGQGTIGLEVLQELPD----VANILVPIGGGGLIAGIATAIRETHPH 195
           A  V  FDDP V+AGQGT GLE+L +  +    +  ILV  GGGGL AGIATA++   P 
Sbjct: 145 ATLVPSFDDPFVIAGQGTAGLEILDQAAEAGAIIGQILVCCGGGGLTAGIATAVKARAPE 204

Query: 196 VRIIGVETAAAPSAHYSLQKGKIVQV-PVTVTLADGIAVKKPGVNTFPIIRDLVDEVVLV 254
           + +  VE A       SL  G    + P   ++ D +    PG  TFPI + L+   ++V
Sbjct: 205 IALYAVEPAGFDDTARSLASGVRENIAPDARSICDALMAPSPGAMTFPINQALLSGGLVV 264

Query: 255 EEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVCVLSGGNIDVKTISVV 314
            ++++  A+       KL+VE  GAV LAA+LN         +V VLSG N+D    + +
Sbjct: 265 SDDQVRDAMRFAFSTLKLVVEPGGAVALAAVLNGLAPPCGDASVVVLSGSNVDPAAYAAI 324

Query: 315 V 315
           V
Sbjct: 325 V 325


Lambda     K      H
   0.319    0.137    0.383 

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: 266
Number of extensions: 16
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: 402
Length of database: 330
Length adjustment: 29
Effective length of query: 373
Effective length of database: 301
Effective search space:   112273
Effective search space used:   112273
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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