Align ABC-type sugar transport system, periplasmic component protein (characterized, see rationale)
to candidate H281DRAFT_03378 H281DRAFT_03378 monosaccharide ABC transporter substrate-binding protein, CUT2 family
Query= uniprot:D8J113 (312 letters) >FitnessBrowser__Burk376:H281DRAFT_03378 Length = 315 Score = 154 bits (390), Expect = 2e-42 Identities = 102/317 (32%), Positives = 166/317 (52%), Gaps = 8/317 (2%) Query: 1 MFKNKLLGAALGLAFAMGASAAQAQEAYIPLISKGFQHQFWQAVKAGADQAGKDYK-VKV 59 M K +L AA + AM ++ AQA I +I K +WQ V+ GA A D K + Sbjct: 1 MKKVSVLAAAAAMC-AMFSAYAQAAGGEIAVIVKTANSNYWQNVQKGATAAMADAKGYTM 59 Query: 60 TFEGPETEAMVDKQIDMLSAALAKKPQAIGFAALDSKAAIPLLKKAQAAKIPVVAFDSGV 119 TF+GP E+ + +++M+ A+ + I A D A +P +KKA A IPVV DS V Sbjct: 60 TFQGPAAESAIADEVNMVENAVNRHVAGIVLAPSDPDALVPAMKKAWEAHIPVVLIDSTV 119 Query: 120 DS---DIPVTTATTDNRAAAALAADKMAELVGKEGEVAVVAHDQTSRTGVDRRDGFLERI 176 + +TDN A L A M + VG+ G+VAV+++ + + V R GF + I Sbjct: 120 SDAGKQYYQSFLSTDNVKAGELCAKAMIDRVGQTGKVAVMSYVPGAGSEVGRVGGFRKYI 179 Query: 177 KSAYPKIKVVSVQYGAGDQLKSTEVTKSILQAYPKIKGIFGTNEGSAIGVVNGVKEMKR- 235 +A+ K+++V Y + T +L A P +KGIFG NE +A+G+ +++ + Sbjct: 180 -AAHSKLQLVGPFYSQSQMANALNQTTDVLSANPDLKGIFGANEPTAVGMGRALQQSGKG 238 Query: 236 -KIIIIGYDSGKQQKDAIREGIMAGAITQNPVGIGYKTVEAAVKAIKGEKLPKVIDTGFY 294 K+I IG+D + + +R+G + Q+ +GYK ++ V I+ + + K +DTG Sbjct: 239 GKVIAIGFDGNQDLQGFVRDGTIQAIAVQSSYQMGYKGIQTLVNVIERKPVSKQVDTGVM 298 Query: 295 WYDKSNIDDAKIAAVLY 311 +K N+D ++ VLY Sbjct: 299 MVEKQNLDSSEAKNVLY 315 Lambda K H 0.315 0.131 0.361 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: 219 Number of extensions: 14 Number of successful extensions: 4 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: 312 Length of database: 315 Length adjustment: 27 Effective length of query: 285 Effective length of database: 288 Effective search space: 82080 Effective search space used: 82080 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 (21.6 bits) S2: 48 (23.1 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