GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Halomonas xinjiangensis TRM 0175

Align L-threonine 3-dehydrogenase; TDH; EC 1.1.1.103 (uncharacterized)
to candidate WP_043527898.1 JH15_RS05915 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase

Query= curated2:Q65JE7
         (346 letters)



>NCBI__GCF_000759345.1:WP_043527898.1
          Length = 369

 Score =  127 bits (318), Expect = 6e-34
 Identities = 110/370 (29%), Positives = 165/370 (44%), Gaps = 51/370 (13%)

Query: 14  EPGASFELVPI----PKIDKHEVLIKVKAASICGTDVHIYNWDEWAKSRVKPPYVFGHEF 69
           E G   EL  I    PK    EVL+++KA S+C TD    +    A      P V GHE 
Sbjct: 10  EAGKPLELTEIEVDGPKAG--EVLVQIKATSVCHTDAFTLSG---ADPEGLFPSVLGHEG 64

Query: 70  SGEVVQVGENVTTVKEGEYVSAETHIVCGKCLPCLTGKEHVC---KKTLILGVDTDG--- 123
           +G V +VGE VT++K G++V       CGKC  CL+GK ++C   + T   GV  DG   
Sbjct: 65  AGIVQEVGEGVTSLKPGDHVIPLYTAECGKCKFCLSGKTNLCSAVRATQGRGVMPDGTSR 124

Query: 124 ---------------CFAEYVKMPAANIWKNPAGMPEDL-----ASIQEPLGNAVHTVLT 163
                           F+EY  +P  ++ K     P D        +   +G  ++T   
Sbjct: 125 FSLNGQTLHHYMGCSTFSEYTVLPEVSLAKVSPEAPLDKICLLGCGVTTGIGAVMNT--A 182

Query: 164 GMTAGVKVAVVGCGPIGLMAVAVAKASGAAQVIAIDKNEYRLDLALQMGATDIIS-VEKE 222
            +  G  VAV G G IGL  +  A+  GA+++IAID N  + +LA Q GATD ++  +  
Sbjct: 183 KVEPGSTVAVFGLGAIGLAVIQGAQMVGASRIIAIDINADKFELARQFGATDFVNPKDHA 242

Query: 223 DPLKNVSALTNGEGADLVCEMSGHPTAIRQSLKMAANGGRVHVL--------SLPEHPVC 274
           DP++ V       G D   E  G+   +RQ+L+    G    V+         +   P  
Sbjct: 243 DPIQQVIVDMTDGGVDYSFECIGNVNVMRQALECCHKGWGESVIIGVAGAGEEISTRP-- 300

Query: 275 IDMTNDIVFKGLTVQGITGRKMFETWRQVSGLLQSGTIQIKPVITHRFPMEEFEKGFELM 334
             +    V++G    G+ GR     + +       G I+I   +TH  P E+  + FEL+
Sbjct: 301 FQLVTGRVWRGSAFGGVKGRTELPGYVE---RYMKGEIKIDEFVTHDMPFEQINEAFELL 357

Query: 335 RKGQCGKVVL 344
             G+  + VL
Sbjct: 358 HAGKSIRSVL 367


Lambda     K      H
   0.318    0.136    0.410 

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: 359
Number of extensions: 24
Number of successful extensions: 5
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: 346
Length of database: 369
Length adjustment: 29
Effective length of query: 317
Effective length of database: 340
Effective search space:   107780
Effective search space used:   107780
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