GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tdcB in Azospirillum brasilense Sp245

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate AZOBR_RS06795 AZOBR_RS06795 serine/threonine dehydratase

Query= BRENDA::Q74FW6
         (402 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS06795 AZOBR_RS06795
           serine/threonine dehydratase
          Length = 331

 Score =  205 bits (521), Expect = 2e-57
 Identities = 123/313 (39%), Positives = 175/313 (55%), Gaps = 9/313 (2%)

Query: 7   IQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREA 66
           I EA  RL     RT L+ +   +E++G  +  K E LQR+G+FK RGA N ++    E 
Sbjct: 14  IVEAAARLDGFAVRTPLLENALLNERVGGRVLLKPEVLQRSGSFKFRGAFNRLSQLTPEE 73

Query: 67  LAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDE 126
              GV+  S+GNHAQGVA +A LLG+P+ + MP   P  K+  TR YGAEVVL  R  + 
Sbjct: 74  RRGGVVAWSSGNHAQGVAAAAALLGMPAVIVMPSDAPALKIANTRGYGAEVVLYDRWTES 133

Query: 127 AYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQE------LPDVANILVPIGGGG 180
             A A    EERGA  V P+D P +MAGQGT+GLE+  +      +PD  +++ P  GGG
Sbjct: 134 REAIATAIAEERGAATVPPYDHPQIMAGQGTVGLEIAAQAQAIGAVPD--DVIAPCSGGG 191

Query: 181 LIAGIATAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQ-VPVTVTLADGIAVKKPGVN 239
           L++G+ATA+R + P  R+   E A       SL  G+ V+      ++ D +    PG  
Sbjct: 192 LMSGVATAVRHSFPDARLWAAEPAGFDDVARSLAAGERVENAAGQRSICDALLTPTPGAL 251

Query: 240 TFPIIRDLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVC 299
           TFP+++DL+   + V + E+  A+       KL+VE  GAV LAA+L  ++         
Sbjct: 252 TFPVMKDLLSGSLAVTDAEVKAAMAYAFTVLKLVVEPGGAVGLAAVLTGKLPAAGRTVAV 311

Query: 300 VLSGGNIDVKTIS 312
           VLSGGN+D  T +
Sbjct: 312 VLSGGNVDAATFT 324


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: 289
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: 402
Length of database: 331
Length adjustment: 30
Effective length of query: 372
Effective length of database: 301
Effective search space:   111972
Effective search space used:   111972
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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