GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcE in Desulfoscipio geothermicus DSM 3669

Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate WP_092483962.1 BM299_RS10985 FAD-linked oxidase C-terminal domain-containing protein

Query= reanno::Smeli:SMc00833
         (405 letters)



>NCBI__GCF_900115975.1:WP_092483962.1
          Length = 458

 Score =  102 bits (253), Expect = 3e-26
 Identities = 85/289 (29%), Positives = 125/289 (43%), Gaps = 20/289 (6%)

Query: 7   PASEEGIASVVRSAAAERVTLAVVGGGTRAGLGN-PVRADRTLSTRRLSGIVTYDPAEMT 65
           P +   +A +VR A  +   +   G GT    G+ P      +   R++ I+     ++ 
Sbjct: 45  PGNAREVAEIVRLANEKGFPIFPRGAGTGLSGGSVPAEQGLAMVLSRMNRILEISRDDLL 104

Query: 66  MSALAGTPVAEVEAALHAKGQMLSFEPMDHRPIFATTGEPTIGGVFAANVSGPRRYVAGA 125
                G     +  A+  +G     +P   +         TIGG  A N  GPR +  G 
Sbjct: 105 AVVEPGVVTGRLHRAVEKEGLFYPPDPSSLQTC-------TIGGNVAENAGGPRAFKYGV 157

Query: 126 ARDSLLGVRFVNGRGEPIKAGGRVMKNVTGLDLVKLMAGSYGTLGILTEVTFKVLPLPPA 185
            RD +LG+  V   GE I  GGR +KNVTG DL  L+ GS GTLGI+T +T +++P P A
Sbjct: 158 TRDYVLGLEVVTPTGEIINTGGRTVKNVTGYDLTGLLTGSEGTLGIITRITLRLVPKPRA 217

Query: 186 AATVVVSGLNDAEAAAVMAEAMAQPVEVSGASHLPESVRSRFLDGAL------PDGAATV 239
             T  ++  N  E AA    AM +   +     L + +  R ++  L        GA  +
Sbjct: 218 VQT-ALAVYNRVEDAASTVTAMIRRGIIPATLELMDRITIRCVENYLRLGLPMDAGAILL 276

Query: 240 LRLEGLAASVAIRAEKLGEKLSRFGRISQL----DEAQTRTLWAEIRDV 284
           + ++GL A VA    KL E   R      L    D A+   LW   R V
Sbjct: 277 IEVDGLPAQVA-EEMKLVEDACRQNSCRALQTATDAAERERLWKARRAV 324


Lambda     K      H
   0.318    0.134    0.387 

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: 455
Number of extensions: 26
Number of successful extensions: 1
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: 405
Length of database: 458
Length adjustment: 32
Effective length of query: 373
Effective length of database: 426
Effective search space:   158898
Effective search space used:   158898
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. 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