Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate GFF2762 PGA1_c28050 putative sugar transport system, permease protein
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__Phaeo:GFF2762 Length = 353 Score = 120 bits (300), Expect = 7e-32 Identities = 100/326 (30%), Positives = 161/326 (49%), Gaps = 42/326 (12%) Query: 19 PTGMPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPID---ILNRAAPVALLAIGMTL 75 P+ +P +V +L V++ L+ G F SP IL + V ++A +L Sbjct: 40 PSLVPLIVLVLSVIVFGLLL-----------GSKFFSPFALTLILQQVGIVGIVACAQSL 88 Query: 76 VIATGGIDLSVGAVMAIAGATTAAMTVAGFSLPIVLLSALGT--GILAGLWNGILVAILK 133 VI T GIDLSVGA+M ++ T + LP + A G G + G NG LVA +K Sbjct: 89 VILTAGIDLSVGAIMVLSSVVMGQFTFR-YGLPPEVAVACGLICGTICGFINGWLVARMK 147 Query: 134 IQPFVATLILMVAGRGVAQLITAG------------QIVTFNSPDLSWFGS----GSLLF 177 + PF+ TL G+ Q++ A Q + +P L FG G +F Sbjct: 148 LPPFIVTL-------GMWQIVLASNFLYSANETIRSQTIAAEAPLLQLFGEKIKIGGAVF 200 Query: 178 LPTPVIIAVLTLILFWLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCA 237 + + +L ++L ++L R TA G + AVG + AA+ +GV +++ Y+LSGL Sbjct: 201 TYGVIFMVILVVLLAYVL-RHTAWGRHVYAVGDDPEAAELSGVKVTRVLISVYMLSGLIC 259 Query: 238 AIAGIIVAADIRGADANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNT 297 A AG + I G+ + +G +++I AVVIGG SL GGR ++L + GALI+ Sbjct: 260 AFAGWAMIGRI-GSVSPTSGQLANIESITAVVIGGISLFGGRGSILGTFFGALIVGVFTL 318 Query: 298 GILLSGFPPEMNQVVKAVVVLCVLIV 323 G+ L G + ++ ++++ + V Sbjct: 319 GLRLLGADAQWTYLLIGLLIIAAVAV 344 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: 271 Number of extensions: 17 Number of successful extensions: 6 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: 353 Length adjustment: 29 Effective length of query: 312 Effective length of database: 324 Effective search space: 101088 Effective search space used: 101088 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