GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Lutibaculum baratangense AMV1

Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate WP_023431610.1 N177_RS07140 glucose 1-dehydrogenase

Query= uniprot:B2T9V3
         (247 letters)



>NCBI__GCF_000496075.1:WP_023431610.1
          Length = 259

 Score =  124 bits (311), Expect = 2e-33
 Identities = 97/261 (37%), Positives = 134/261 (51%), Gaps = 24/261 (9%)

Query: 4   RLAGKTALITAAGQGIGLATAELFAREGARVIATDIRID-------GLAGKPVEARKL-- 54
           R+  K AL+T    G+G ATA L AREGA+V+ TDI+ +        +A    EA  L  
Sbjct: 3   RVKDKVALVTGGSVGLGEATARLLAREGAKVVVTDIQDEKGETVARDIAAAGGEALYLHH 62

Query: 55  DVRDDAA----IKALAAEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRMI 110
           DV D+AA    I A     G +DVL N AG        E + EDW     +N+  ++   
Sbjct: 63  DVADEAAWEQVIAATVERFGRLDVLVNNAGIGTGCPPEEQTLEDWRRLMSINLDGVFLGT 122

Query: 111 RAFLPAML---DKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRG- 166
           +  + AM        GSI+N+SS    V G PN  AY+ASK  V   TKSVA      G 
Sbjct: 123 KHAILAMKAHKPMTQGSIVNLSSIEGLV-GDPNLGAYNASKGGVRIYTKSVALYCAKEGL 181

Query: 167 -VRCNAICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALY 225
            +R N++ PG + +P +E  +      +   L+  +A   A  P+G +G+P++IA   LY
Sbjct: 182 GIRANSVHPGYIWTPMVENYL-----RENDNLEEGRAQLDALHPIGHVGEPDDIAYGVLY 236

Query: 226 LGSDESSFTTGHAHVIDGGWS 246
           L SDES F TG   VIDGG++
Sbjct: 237 LASDESKFVTGTELVIDGGYT 257


Lambda     K      H
   0.320    0.133    0.381 

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: 177
Number of extensions: 10
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: 247
Length of database: 259
Length adjustment: 24
Effective length of query: 223
Effective length of database: 235
Effective search space:    52405
Effective search space used:    52405
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: 46 (22.3 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