Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate SM_b20352 SM_b20352 sugar ABC transporter permease
Query= uniprot:B2T9V8 (351 letters) >FitnessBrowser__Smeli:SM_b20352 Length = 354 Score = 179 bits (453), Expect = 1e-49 Identities = 103/318 (32%), Positives = 173/318 (54%), Gaps = 9/318 (2%) Query: 33 SELARLRELALLPALALLIVIGAFISPSFLTKANLISVLGASAALALVVLAESLIVLTGK 92 S L L +L AL ++ + +P+FL+ ANLI + A A + + + +++TG Sbjct: 17 SVLLTLMKLRTFIALFAVVAFFSIFAPNFLSTANLILMSKHVALNAFLAMGMTFVIITGG 76 Query: 93 FDLSLESTVGIAPAVGAMLVMPAASAGFG--MQWPAAAGLLAIVVVGAVIGFINGFLVVR 150 DLS+ S VG+ V L++ FG + + L + VG VIG +NG L+ + Sbjct: 77 IDLSVGSIVGLCGMVAGGLILNGIDLQFGYTVYFNVVEVCLITLAVGIVIGAVNGLLITK 136 Query: 151 LRLNAFIVTLAMLIVLRGMLVGATKGGTLFDM-------PTSFFALATTIVLGLPLSVWL 203 L + FI TL L V RG + ++ G T ++ T F L + +LGLP+S+W+ Sbjct: 137 LNVAPFIATLGTLYVARGFALLSSGGQTFPNLVGKPELATTGFAFLGSGRLLGLPVSIWV 196 Query: 204 AAAAFAIAAFMLRYHRLGRALYAIGGNPEAARAAGIRVERITWGVFVLGSILASVGGLIV 263 AA++ RY +GR ++A+GGN AAR +GIRV+R+ V++ A++ GL++ Sbjct: 197 LIVVALAAAYVARYTPIGRHIFAVGGNERAARMSGIRVDRVKMFVYMFSGFCAAIVGLVI 256 Query: 264 TGYVGAINANQGNGMIFTVFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLTLAQVP 323 + + A + GN AAAV+GG S+ GG+GT+ G + G ++G++ + L + + Sbjct: 257 SSELMASHPATGNSFELNAIAAAVLGGTSMSGGRGTIGGTIIGAFVIGILSDGLVMMGIS 316 Query: 324 SFWIQAIYGAIILGSLMV 341 SFW I G +I+ +++V Sbjct: 317 SFWQMVIKGIVIIVAVVV 334 Lambda K H 0.326 0.140 0.397 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: 324 Number of extensions: 15 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: 351 Length of database: 354 Length adjustment: 29 Effective length of query: 322 Effective length of database: 325 Effective search space: 104650 Effective search space used: 104650 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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