GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Frischella perrara PEB0191

Align sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14) (characterized)
to candidate WP_039104375.1 FPB0191_RS04620 SDR family oxidoreductase

Query= reanno::BFirm:BPHYT_RS16120
         (260 letters)



>NCBI__GCF_000807275.1:WP_039104375.1
          Length = 246

 Score =  108 bits (270), Expect = 1e-28
 Identities = 76/252 (30%), Positives = 125/252 (49%), Gaps = 17/252 (6%)

Query: 8   KVAILTGAASGIGEAVARRYLDEGARCVLVDVKPADSFGDSLRATYGDRVLTVSADVTRR 67
           K  I+TGA+SGIG A+ + YLD+G   V            + +      +L V+ D++  
Sbjct: 5   KTVIVTGASSGIGFAITKAYLDQGYNVVANGRDKGRLDEAAKQLGQPTNLLLVAGDISLP 64

Query: 68  DDIQRIVASTLERFGQIDILFNNAALFDMRPILEESWDVFDRLFAVNVKGMFFLMQAVAQ 127
           +  + +     + FG+IDIL NNA +F  +PI + + +  D +   N+KG F+  Q +A 
Sbjct: 65  ETAKSLFTLAQKHFGKIDILVNNAGIFISKPISQYTAEDLDNIINTNLKGFFYPTQ-LAV 123

Query: 128 KMVEQGCGGKIINMSSQAGRRGEALVSHY--CATKAAVLSYTQSAALALAPHKINVNGIA 185
           + ++   GG I+N+++    +    V       TK A+ S  +  AL LA   I VNGIA
Sbjct: 124 EYMKPNKGGHIVNITAAIALQPNLAVPALLPIMTKGAINSAIKGLALELANDNIRVNGIA 183

Query: 186 PGVVDTPMWNEVDALFARYENRPLGEKKRLVGEAVPLGRMGVPDDLTGAALFLASADADY 245
           PG++ TPM  +        +++ L   K L     P   +G   D+  A L+L   D+ +
Sbjct: 184 PGIIQTPMHTQ--------DHQSLSMLKSL----CPSNNIGQVTDIVDAVLYL--TDSQF 229

Query: 246 ITAQTLNVDGGN 257
           +T   + VDGG+
Sbjct: 230 VTGTVMVVDGGS 241


Lambda     K      H
   0.321    0.135    0.393 

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: 142
Number of extensions: 7
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: 260
Length of database: 246
Length adjustment: 24
Effective length of query: 236
Effective length of database: 222
Effective search space:    52392
Effective search space used:    52392
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 (21.9 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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:

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