GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Desulfotomaculum hydrothermale Lam5

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_008410242.1 DESHY_RS02740 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA

Query= BRENDA::Q97UY8
         (353 letters)



>NCBI__GCF_000315365.1:WP_008410242.1
          Length = 263

 Score =  149 bits (375), Expect = 1e-40
 Identities = 87/240 (36%), Positives = 144/240 (60%), Gaps = 14/240 (5%)

Query: 4   IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63
           +I +NV K F  GK+  L  +++ ++ GE   I+GPSG+GK+TF+R I  L+   +G + 
Sbjct: 2   VIAENVRKNF--GKLQVLKGISLEVKQGEVVVIIGPSGSGKSTFLRCINHLEARDSGVVE 59

Query: 64  FDDRLVA---SNGKLIVPPEDR-------KIGMVFQTWALYPNLTAFENIAF-PLTNMKM 112
            D + V    S G  ++P + +        IGMVFQ + L+P++TA  N+   P+T +  
Sbjct: 60  VDGQPVGFSQSAGGRLLPVKGKDLCRLRSSIGMVFQRFNLFPHMTALANVMEGPVTVLGK 119

Query: 113 SKEEIRKRVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLD 172
           S++E R+  EE+   + +    + FP +LSGGQQQRVA+ARAL   P L+L DEP S LD
Sbjct: 120 SRQEARQLAEELLAKVGLADKADSFPSQLSGGQQQRVAIARALAMKPKLMLFDEPTSALD 179

Query: 173 ARMRDSARALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNP 232
             +     A++K + +  G+T+++V+H+      +ADRV  + +GK+++ G PE ++ +P
Sbjct: 180 PELVGEVLAVIKNLAAE-GMTMIIVTHEMGFAREVADRVVFMDEGKIIESGTPEQIFTSP 238


Lambda     K      H
   0.319    0.139    0.390 

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: 259
Number of extensions: 12
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 353
Length of database: 263
Length adjustment: 27
Effective length of query: 326
Effective length of database: 236
Effective search space:    76936
Effective search space used:    76936
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 (21.7 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