Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate HSERO_RS03645 HSERO_RS03645 ribose ABC transporter permease
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__HerbieS:HSERO_RS03645 Length = 339 Score = 184 bits (468), Expect = 2e-51 Identities = 110/275 (40%), Positives = 164/275 (59%), Gaps = 9/275 (3%) Query: 57 IDILNRAAPVALLAIGMTLVIATGGIDLSVGAVMAIA---GATTAAMTVAGFSLPIVLLS 113 ++IL + A +LA GMT VI T GIDLSVG+V+A++ G + G+++P+ + S Sbjct: 62 MNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVSLGAAPGWAIPMFIFS 121 Query: 114 ALGTGILAGLWNGILVAILKIQPFVATLILMVAGRGVAQLITAGQIVTFNS-PDLSWFGS 172 G++ G+ NG +VA+L I FV TL M A RG A L+ G V N P W G+ Sbjct: 122 ----GLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNNDIPSFEWIGN 177 Query: 173 GSLLFLPTPVIIAVLTLILFWLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVL 232 G L +P + +AV ++L W++ RKT LGM I A+G N++AA+ G+ ++++ Y + Sbjct: 178 GDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSI 237 Query: 233 SGLCAAIAGIIVAADIRGADANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALII 292 SGL + +AG + A+ + GA+ N G ELDAI AVV+GG SLMGG ++ +VVGALII Sbjct: 238 SGLFSGLAGAMSASRLYGAN-GNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALII 296 Query: 293 QGMNTGILLSGFPPEMNQVVKAVVVLCVLIVQSQR 327 MN G+ + G V K V++ +I+ R Sbjct: 297 GVMNNGLTILGLSSFWQYVAKGAVIVLAVILDKWR 331 Lambda K H 0.327 0.142 0.416 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: 295 Number of extensions: 24 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: 341 Length of database: 339 Length adjustment: 28 Effective length of query: 313 Effective length of database: 311 Effective search space: 97343 Effective search space used: 97343 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 (21.7 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