GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Marinobacter adhaerens HP15

Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate GFF4077 HP15_4017 formaldehyde dehydrogenase (glutathione-dependent)

Query= BRENDA::O58389
         (348 letters)



>FitnessBrowser__Marino:GFF4077
          Length = 370

 Score =  130 bits (326), Expect = 7e-35
 Identities = 113/378 (29%), Positives = 181/378 (47%), Gaps = 49/378 (12%)

Query: 2   SEKMVAIMKTKPGYGAELVEVDVPKPGPGEVLIKVLATSICGTDLHIYEWNEWAQSRIKP 61
           S   VA    KP    E+VEVDV  P  GEVL++++AT +C TD +       A      
Sbjct: 4   SRAAVAFEANKP---LEIVEVDVAPPQEGEVLVRIVATGVCHTDAYTLSG---ADPEGLF 57

Query: 62  PQIMGHEVAGEVVEIGPGVEGIEVGDYVSVETHIVCGKCYACRRGQYHVC---QNTKIFG 118
           P I+GHE  G V  +GPGV+ +EVGD+V       CG+C  C  G+ ++C   + T+  G
Sbjct: 58  PTILGHEGGGIVEAVGPGVKNLEVGDHVIPLYTAECGECKFCTSGKTNLCGAVRATQGKG 117

Query: 119 VDTDG------------------VFAEYAVVPAQNIWKNPKSIPPEYATLQEPLGNAVDT 160
           V  DG                   F+EY V+P  ++ K PK  P +   L   LG  V T
Sbjct: 118 VMPDGTSRFSYNGQPLYHYMGCSTFSEYTVLPEISLAKIPKDAPLDKVCL---LGCGVTT 174

Query: 161 VLAGPIS------GKSVLITGAGPLGLLGIAVAKASGAYPVIVSEPSDFRRELAKKVGAD 214
            +   ++      G +V I G G +GL  I  AK + A  +I  + +  + ++AK++GA 
Sbjct: 175 GIGAVLNTAKVEEGATVAIFGLGGIGLAAIIGAKMAKAGRIIGVDINPGKFDIAKQLGAT 234

Query: 215 YVINP--FEEDVVKEVMDITDGNGVDVFLEFSGAPKALEQGLQAVTPA-GRVSLLGLYPG 271
            V+NP  +++ + + ++D+TDG G D   E  G  K +   L+A     G  +++G+   
Sbjct: 235 DVVNPNDYDKPIQEVIVDMTDG-GADYTFECVGNVKLMRAALEACHKGWGESTIIGVAGA 293

Query: 272 KVTIDFN--NLI---IFKALTIYGITGRHLWETWYTVSRLLQSGKLNLDPIITHKYKGFD 326
              I      L+   +++     G+ GR     +   +   + G++ LD  ITH+    +
Sbjct: 294 GEEISTRPFQLVTGRVWRGSAFGGVKGRTELPGYVEKA---EKGEIPLDVFITHEMP-LE 349

Query: 327 KYEEAFELMRAGKTGKVV 344
              +AF+LM  GK+ + V
Sbjct: 350 DINKAFDLMHEGKSIRTV 367


Lambda     K      H
   0.318    0.139    0.418 

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: 358
Number of extensions: 23
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: 348
Length of database: 370
Length adjustment: 29
Effective length of query: 319
Effective length of database: 341
Effective search space:   108779
Effective search space used:   108779
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 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