Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate N515DRAFT_2415 N515DRAFT_2415 simple sugar transport system permease protein
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__Dyella79:N515DRAFT_2415 Length = 337 Score = 123 bits (309), Expect = 6e-33 Identities = 92/258 (35%), Positives = 138/258 (53%), Gaps = 18/258 (6%) Query: 57 IDILNRAAPVALLAIGMTLVIATGGIDLSVGAVMAIAGATTAAMTVAGFSLP---IVLLS 113 +++L A + ++A+GMT VI GGIDLSVGAV+A + A + P I L+ Sbjct: 55 LNLLIDNAFLCIVAVGMTFVILAGGIDLSVGAVVAFSTVLLAELVQRHGWPPLAAIALVL 114 Query: 114 ALGTGILAGLWNGILVAILKIQPFVATLILMVAGRGVAQLITAGQIVTFNSPDLSWFGSG 173 A+GTG AG+ G+L+ ++QPFV TL M RGVA LI+ I D W S Sbjct: 115 AVGTGFGAGM--GVLIQRFRLQPFVVTLAGMFLARGVATLISVDSI----DIDQPWLASV 168 Query: 174 SLLFLP--------TPVIIAVLTLILFWLLTRKTALGMFIEAVGINIRAAKNAGVNTRII 225 + L LP ++A+ + LL ++ G + A+G + +A+ G+ Sbjct: 169 ANLRLPLGGGSMLSVGALVALAVVAAGALLAGASSFGRTVYAIGGSESSARLMGLPVDAT 228 Query: 226 VMLTYVLSGLCAAIAGIIVAADIRGADANNAGLWLELDAILAVVIGGGSLMGGRFNLLLS 285 V+ Y LSG CAA+AG++ + + +A L LELDAI AVVIGG L GG +L + Sbjct: 229 VVRVYALSGFCAALAGVVYTLYMLSGYSQHA-LGLELDAIAAVVIGGTVLAGGSGYVLGT 287 Query: 286 VVGALIIQGMNTGILLSG 303 ++G L++ + T I+ G Sbjct: 288 LLGVLVLGLIQTLIVFDG 305 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: 315 Number of extensions: 21 Number of successful extensions: 5 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: 337 Length adjustment: 28 Effective length of query: 313 Effective length of database: 309 Effective search space: 96717 Effective search space used: 96717 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 Apr 09 2024. 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