GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Magnetospirillum magneticum AMB-1

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_011384493.1 AMB_RS10565 ABC transporter ATP-binding protein

Query= BRENDA::Q97UY8
         (353 letters)



>NCBI__GCF_000009985.1:WP_011384493.1
          Length = 257

 Score =  131 bits (330), Expect = 2e-35
 Identities = 82/233 (35%), Positives = 128/233 (54%), Gaps = 14/233 (6%)

Query: 3   RIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGEL 62
           +I +  V K F  G  V LD +++++  GE   ++G SG GK+  ++ I GL  P +G +
Sbjct: 6   KIELTGVHKAF--GPKVVLDGIDLSVARGESVVVIGGSGTGKSVMLKCILGLLRPESGSI 63

Query: 63  YFDDRLVASNGKLIVPPEDR-----KIGMVFQTWALYPNLTAFENIAFPLTN-MKMSKEE 116
             D   V   G     P+DR     K GM+FQ  AL+ +L  +EN+AF L    KM + +
Sbjct: 64  RIDGEDVVGMG-----PKDRDRIMKKFGMLFQGGALFDSLKVWENVAFGLIQGQKMERAK 118

Query: 117 IRK-RVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARM 175
            R   +E++A++          P ELSGG Q+RV+LARA+  +P ++  DEP + LD  M
Sbjct: 119 ARDIAIEKLAQVGLAASTGELSPSELSGGMQKRVSLARAIATNPEIIFFDEPTTGLDPIM 178

Query: 176 RDSARALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDL 228
            D    L+ +    +G T L ++HD A    I+DR+ +L KG+L+ VG  +D+
Sbjct: 179 ADVINDLIVKCCKEVGATALSITHDMASARKISDRIAMLYKGRLIWVGPAKDI 231


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: 231
Number of extensions: 19
Number of successful extensions: 3
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: 353
Length of database: 257
Length adjustment: 27
Effective length of query: 326
Effective length of database: 230
Effective search space:    74980
Effective search space used:    74980
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 17 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