GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Phaeobacter inhibens BS107

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate GFF2690 PGA1_c27320 putative sugar ABC transporter, ATP-binding protein

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Phaeo:GFF2690
          Length = 349

 Score =  203 bits (516), Expect = 6e-57
 Identities = 109/251 (43%), Positives = 162/251 (64%), Gaps = 9/251 (3%)

Query: 1   MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60
           M +I ++N+SK  + G  V +DN ++ I + E   +LGPSG GKTT MR+IAGL+  S G
Sbjct: 1   MAQIELRNISK--RWGSFVGVDNFDLTIADKEFLVLLGPSGCGKTTTMRMIAGLESASEG 58

Query: 61  ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120
           ++  D   V       + P+DR + MVFQ++ALYPN+  +ENI FPL    +  +   ++
Sbjct: 59  DILVDGNRVNE-----LEPKDRDVAMVFQSYALYPNMNVYENIRFPLKVRGVDAKTHDEK 113

Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180
           V   + ++++   L+  P ELSGGQ+QRVALARA+V++P++ L+DEP SNLDA++R S R
Sbjct: 114 VRRASAMVELDEFLHRKPAELSGGQRQRVALARAIVREPNVFLMDEPLSNLDAKLRVSTR 173

Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240
           A +K +   L VT + V+HD  +   +ADRV V+ KG + QVG P ++YD P +  VAS 
Sbjct: 174 AQIKNLSHELAVTTIYVTHDQIEAMTLADRVVVMNKGVVQQVGSPTEIYDRPANAFVASF 233

Query: 241 IGE--INELEG 249
           IG   +N +EG
Sbjct: 234 IGSPAMNLMEG 244


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: 274
Number of extensions: 14
Number of successful extensions: 2
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: 349
Length adjustment: 29
Effective length of query: 324
Effective length of database: 320
Effective search space:   103680
Effective search space used:   103680
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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