GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Vagococcus penaei CD276

Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate WP_077274914.1 BW732_RS00300 D-threitol dehydrogenase

Query= uniprot:B2T9V3
         (247 letters)



>NCBI__GCF_001998885.1:WP_077274914.1
          Length = 254

 Score =  124 bits (311), Expect = 2e-33
 Identities = 83/252 (32%), Positives = 123/252 (48%), Gaps = 21/252 (8%)

Query: 5   LAGKTALITAAGQGIGLATAELFAREGARVIATDIR------IDGLAGKPVEARKLDVRD 58
           L  K A+IT    GIG A  EL+ ++GA++   DI       ++   G       +DV  
Sbjct: 12  LENKVAIITGGLSGIGSAIGELYVKKGAKLAIFDINPDTPELVEEQFGTKAIGFAVDVTS 71

Query: 59  DA----AIKALAAEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRMIRAFL 114
                 A+K        +D+L N AG     +    SE +WD  F++NVK  + + +A  
Sbjct: 72  KEQVMNAVKETMNHFKKIDILVNSAGVCFLDDAENLSETEWDLTFNINVKGSFLVAQAVG 131

Query: 115 PAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCNAICP 174
             M+  GGG IINM+S A+ V  + N  AY+ASK A++ +TK +A ++    +  N + P
Sbjct: 132 NEMIQSGGGKIINMASQAALV-ALDNHVAYAASKGAILSMTKVLAYEWAQYSINVNCLSP 190

Query: 175 GTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDESSFT 234
                      IV     + A    V      + P+GR G PEE+AA AL+L SD S+  
Sbjct: 191 ----------TIVLTELGKKAWAGQVGEDMKQQIPIGRFGYPEEVAASALFLASDASNLM 240

Query: 235 TGHAHVIDGGWS 246
           TG   VIDGG++
Sbjct: 241 TGENMVIDGGYT 252


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: 142
Number of extensions: 7
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: 254
Length adjustment: 24
Effective length of query: 223
Effective length of database: 230
Effective search space:    51290
Effective search space used:    51290
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