Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate AO353_20825 AO353_20825 ABC transporter permease
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__pseudo3_N2E3:AO353_20825 Length = 325 Score = 140 bits (352), Expect = 6e-38 Identities = 90/302 (29%), Positives = 156/302 (51%), Gaps = 11/302 (3%) Query: 27 ALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALLAIGMTLVIATGGIDLSV 86 ALL ++ + S+++ HF + + + N+ + +LA+GMT V+ GGIDLSV Sbjct: 26 ALLAMIALFSVLSSHFLS--------YDTFSTLANQIPDLMVLAVGMTFVLIIGGIDLSV 77 Query: 87 GAVMAIAGATTAAMTVA-GFSLPIVLLSALGTGILAGLWNGILVAILKIQPFVATLILMV 145 G+V+A+AG+T + + G+S+ L + +AG G + +I F+ +L ++ Sbjct: 78 GSVLALAGSTVSVAILGWGWSVLPAALLGMAAAAVAGTITGSITVAWRIPSFIVSLGVLE 137 Query: 146 AGRGVAQLITAGQIVTFNSPDLSWFGSGSLLFLPTPVIIAVLTLILFWLLTRKTALGMFI 205 RGVA +T G + +W + + IIA+L + + + +T G ++ Sbjct: 138 MARGVAYQMT-GSRTAYIGDAFAWLSNPITFGISPSFIIALLVIFIAQAVLTRTVFGRYL 196 Query: 206 EAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGADANNAGLWLELDAI 265 +G N A + AG+N + +L + L GL A IA + + + AD N AG LEL I Sbjct: 197 IGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGIAALFQISRLEAADPN-AGSGLELQVI 255 Query: 266 LAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPPEMNQVVKAVVVLCVLIVQS 325 AVVIGG SLMGGR +++ + G LII + G+ G +++ V++ +++ + Sbjct: 256 AAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAVIVVAVVLDT 315 Query: 326 QR 327 R Sbjct: 316 YR 317 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: 261 Number of extensions: 15 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: 325 Length adjustment: 28 Effective length of query: 313 Effective length of database: 297 Effective search space: 92961 Effective search space used: 92961 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