GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Streptacidiphilus oryzae TH49

Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate WP_063836871.1 BS73_RS00110 SDR family oxidoreductase

Query= uniprot:B2T9V3
         (247 letters)



>NCBI__GCF_000744815.1:WP_063836871.1
          Length = 345

 Score =  165 bits (418), Expect = 1e-45
 Identities = 100/256 (39%), Positives = 144/256 (56%), Gaps = 21/256 (8%)

Query: 5   LAGKTALITAAGQGIGLATAELFAREGARVIATDIRIDGL---------AGKPVEARKLD 55
           L GKTA +T AG GIG A A   A EGARV A DIR+            +G    A + D
Sbjct: 4   LTGKTAFVTGAGSGIGQACALRLAEEGARVAAVDIRLPAAEETAKRIEASGGTAVAVECD 63

Query: 56  VRDD----AAIKALAAEIGAVDVLFNCAGFVHA-GNILECSEEDWDFAFDLNVKAMYRMI 110
           V       AA+      +GA+ V+ N AG + A G+++ CSE+DWD    +NVK+MY + 
Sbjct: 64  VSSGRQVAAAVSRTVEALGALHVIVNAAGILAAEGDVVACSEDDWDRVMGVNVKSMYLIG 123

Query: 111 RAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCN 170
           +  +P +L  GGGSI+N++S       +P+  AY ASK AV+ LT+ +A  +  +G+R N
Sbjct: 124 KHGVPEILRAGGGSIVNIAS-VFGFTALPDECAYDASKGAVLNLTRQMAVQYAKQGIRVN 182

Query: 171 AICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDE 230
           A+CP    +P L+      A   G  ++A +A      PMGR+ +PEEIA+   +L SD+
Sbjct: 183 ALCPSDCDTPLLD------ALLAGGDVEAEKAELAKPIPMGRLARPEEIASGVAFLASDD 236

Query: 231 SSFTTGHAHVIDGGWS 246
           ++F TG A  +DGG S
Sbjct: 237 AAFVTGVALPVDGGSS 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: 234
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: 345
Length adjustment: 26
Effective length of query: 221
Effective length of database: 319
Effective search space:    70499
Effective search space used:    70499
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: 48 (23.1 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