GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS06795
          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:

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