Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate PfGW456L13_4204 ABC transporter, ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4204 Length = 329 Score = 197 bits (501), Expect = 3e-55 Identities = 117/288 (40%), Positives = 174/288 (60%), Gaps = 21/288 (7%) Query: 1 MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60 M + V+++ K F V + ++N I+ GE +LGPSG GK+T +R IAGL G Sbjct: 1 MSYVSVQHLQKSFAGTTVFS--DINCEIQKGEFVTLLGPSGCGKSTLLRCIAGLTSVDGG 58 Query: 61 ELYFDDRLVASNGKLIVP--PEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIR 118 ++ D G IVP P+ R IGMVFQ++AL+PN+T +N+AF L K++ ++ R Sbjct: 59 KILLD-------GADIVPVSPQKRGIGMVFQSYALFPNMTVEQNVAFGLRMQKVNADDSR 111 Query: 119 KRVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDS 178 KRV EV K+++++ +P +LSGGQ QRVALAR+LV P LLLLDEP S LDAR+R Sbjct: 112 KRVAEVLKLVELNDFAARYPHQLSGGQCQRVALARSLVTRPRLLLLDEPLSALDARIRKH 171 Query: 179 ARALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVA 238 R ++++Q LG+T + V+HD + ++DR+ ++ +GK+VQ G E LY PV + A Sbjct: 172 LREQIRQIQRELGLTTIFVTHDQEEALTMSDRIFLMNQGKIVQSGDAETLYTAPVDVFAA 231 Query: 239 SLIGEINELEGKVTNEGVVIGSLRFPVSVSSDRAIIGIRPEDVKLSKD 286 IG N L+ ++ L+ P++ I IRPE ++LS D Sbjct: 232 GFIGNYNLLDADSASK-----LLQRPINKR-----IAIRPEAIELSLD 269 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: 11 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: 329 Length adjustment: 28 Effective length of query: 325 Effective length of database: 301 Effective search space: 97825 Effective search space used: 97825 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.
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:
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