GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdcB in Lutibaculum baratangense AMV1

Align threonine ammonia-lyase; EC 4.3.1.19 (characterized)
to candidate WP_051402369.1 N177_RS12980 threonine/serine dehydratase

Query= CharProtDB::CH_024588
         (329 letters)



>NCBI__GCF_000496075.1:WP_051402369.1
          Length = 340

 Score =  222 bits (566), Expect = 9e-63
 Identities = 134/326 (41%), Positives = 192/326 (58%), Gaps = 10/326 (3%)

Query: 6   DLPVAIDDIIEAKQRLAGRIYKTGMPRSNYFSERCKGEIFLKFENMQRTGSFKIRGAFNK 65
           DLP + DD+  A +RL+G   +T + RS    ER    + LK E +QRTGSFK RGA+N 
Sbjct: 18  DLP-SFDDVRRASERLSGEAVRTPLVRSAILDERAGRPVLLKAEVLQRTGSFKFRGAYNA 76

Query: 66  LSSLTDAEKRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDYSAEVV 125
           ++SL    + KGVVACS+GNHAQGV+ +  + G+   +VMP  AP  KVA T    A VV
Sbjct: 77  IASLDADARAKGVVACSSGNHAQGVAEAARLFGVRATIVMPADAPALKVARTKRSGAHVV 136

Query: 126 LHGDNFNDTIAKVS-EIVEMEGRIFIPPYDDPKVIAGQGTIGLEIMEDL----YDVDNVI 180
            + D  N++  +++  IV   G  F+PPYDD +VI+GQGT+G+EI E       D   ++
Sbjct: 137 TY-DRVNESREEIALRIVAETGADFVPPYDDRRVISGQGTVGIEIAEQAEALGLDPARIL 195

Query: 181 VPIGGGGLIAGIAVAIKSINPTIRVIGVQSENVHGMAASFHSGEITTHRT-TGTLADGCD 239
           VP  GGGL AGIA+A +++ P  RV  V+ E     A SF SGE   +   +G++ D   
Sbjct: 196 VPCSGGGLSAGIALAAEALMPWARVTTVEPEAFDDHARSFRSGEREGNTARSGSICDALL 255

Query: 240 VSRPGNLTYEIVRELVDDIVLVSEDEIRNSMIALIQRNKVVTEGAGALACAALLSGKLDQ 299
             RPG +T+ + R  V   + VS+DE+R +M    +  K+V E  GA+  AA+L+G+LD+
Sbjct: 256 ADRPGEITFAVNRPRVPSGLAVSDDEVRTAMRFAFEELKLVVEPGGAVGLAAVLAGRLDE 315

Query: 300 YIQNRKTVSIISGGNIDLSRVSQITG 325
             Q    V ++SGGN   S  ++  G
Sbjct: 316 GPQ--PVVVVLSGGNAGPSAYAEAIG 339


Lambda     K      H
   0.318    0.136    0.386 

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: 245
Number of extensions: 11
Number of successful extensions: 3
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: 329
Length of database: 340
Length adjustment: 28
Effective length of query: 301
Effective length of database: 312
Effective search space:    93912
Effective search space used:    93912
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 (21.7 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