GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fucDH in Paraburkholderia bryophila 376MFSha3.1

Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate H281DRAFT_06296 H281DRAFT_06296 NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family

Query= SwissProt::Q8P3K4
         (300 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_06296 H281DRAFT_06296
           NAD(P)-dependent dehydrogenase, short-chain alcohol
           dehydrogenase family
          Length = 258

 Score =  156 bits (395), Expect = 4e-43
 Identities = 105/254 (41%), Positives = 142/254 (55%), Gaps = 11/254 (4%)

Query: 55  TRLQGKRCLITAAGAGIGRESALACARAGAHVIAT--DIDAA--ALQALAAESDA-ITTQ 109
           TRL GK  L+T AG GIG   ALA AR GA V     DID A    Q +++E+ A +   
Sbjct: 2   TRLAGKVALVTGAGRGIGAAIALAFAREGAAVALAELDIDTARQTAQQISSETGARVLAV 61

Query: 110 LLDVTDAAAITALVAAH----GPFDVLFNCAGYVHQGSILDCDEPAWRRSFSINVDAMYY 165
             DVT +A++   V+      GP DVL N AG       L   +  WRR F++++D ++ 
Sbjct: 62  HTDVTQSASVQHAVSEAEKKLGPLDVLVNNAGINVFCDPLTMTDDDWRRCFAVDLDGVWN 121

Query: 166 TCKAVLPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGVR 225
            C+AVLPGM+ERG GSI+N++S   + K +P  F Y V K  VIGL++A+  +Y  + VR
Sbjct: 122 GCRAVLPGMVERGAGSILNIAS-THAFKIIPGCFPYPVAKHGVIGLTRALGIEYAPRNVR 180

Query: 226 CNAICPGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDESS 285
            NAI PG I+T  L         D  A  ++  D QPM R+G P E+A   V+LASDE+ 
Sbjct: 181 VNAIAPGYIET-QLTHDWWNEQPDPAAARQATMDLQPMKRIGRPEEVAMTAVFLASDEAP 239

Query: 286 FTTGQTHIIDGGWS 299
           F       +DGG S
Sbjct: 240 FINATCITVDGGRS 253


Lambda     K      H
   0.320    0.133    0.395 

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: 153
Number of extensions: 8
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: 300
Length of database: 258
Length adjustment: 25
Effective length of query: 275
Effective length of database: 233
Effective search space:    64075
Effective search space used:    64075
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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