GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdcB in Pseudomonas putida KT2440

Align L-threonine dehydratase biosynthetic IlvA; EC 4.3.1.19; Threonine deaminase (uncharacterized)
to candidate PP_4430 PP_4430 putative threonine dehydratase

Query= curated2:P53607
         (507 letters)



>FitnessBrowser__Putida:PP_4430
          Length = 330

 Score =  191 bits (485), Expect = 3e-53
 Identities = 115/303 (37%), Positives = 177/303 (58%), Gaps = 9/303 (2%)

Query: 14  RVYDVAFETELEPARNLSARLRNPVYLKREDNQPVFSFKLRGAYNKMAHIPADALARGVI 73
           R+  +  ET +E + +LS  ++ PVYLK E +Q   SFKLRGA N +A + +   A GV+
Sbjct: 15  RIKHLVRETRMELSPSLSDFMKVPVYLKLECHQATGSFKLRGATNAIAGLTSQQRALGVV 74

Query: 74  TASAGNHAQGVAFSAARMGVKAVIVVPVTTPQVKVDAVRAHGGPGVEVIQAGESYSDAYA 133
           TAS GNH + ++++AA  GV+A + +    P  KV A+RA G   V+V+  G S  DA  
Sbjct: 75  TASTGNHGRALSYAAAAAGVRATVCLSRLVPSNKVAAIRALGA-AVQVV--GNSQDDAQF 131

Query: 134 HALKVQEERGLTFVHPFDDPYVIAGQGTIAMEILRQHQGPIHAIFVPIGGGGLAAGVAAY 193
            A ++ +E GLTF+ PFD   VIAGQ T+ +EI  Q    +  + +P+ GGGL +GV+  
Sbjct: 132 EAARLAQEEGLTFIPPFDHQDVIAGQATLGLEIAEQLPS-VSQVLIPLSGGGLFSGVSLA 190

Query: 194 VKAVRPEIKVIGVQAEDSCAMAQSLQAGKRVELAEVGLFAD--GTAVKLVGEETFRLCKE 251
           +KA+ P++K  GV      AMAQSL+AGK V + EV   AD  G  + L  + TF L + 
Sbjct: 191 LKALLPQVKTHGVSMRLGAAMAQSLEAGKPVNVEEVATLADSLGGGIGLRNQYTFELTRR 250

Query: 252 YLDGVVTVDTDALCAAIKDVFQDTRSVLEPSGALAVAGAKLYAEREGIENQTLVAVTSGA 311
           ++D V+ ++ D++  A+   + + R V+E +GA+ +A       R+      +V V SG 
Sbjct: 251 FIDRVILLNEDSIADAMLHAYLEERLVIEGAGAVGIAA---LLTRQVEAQGPIVIVVSGG 307

Query: 312 NMN 314
           N++
Sbjct: 308 NVD 310


Lambda     K      H
   0.320    0.135    0.388 

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: 313
Number of extensions: 13
Number of successful extensions: 4
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: 507
Length of database: 330
Length adjustment: 31
Effective length of query: 476
Effective length of database: 299
Effective search space:   142324
Effective search space used:   142324
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: 50 (23.9 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