Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__Koxy:BWI76_RS14865 Length = 339 Score = 204 bits (520), Expect = 2e-57 Identities = 114/307 (37%), Positives = 184/307 (59%), Gaps = 9/307 (2%) Query: 17 RWPTGMPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALLAIGMTLV 76 +W + L+ LL++L++ S AP+F +V + ++I + A+LA GMT V Sbjct: 20 KWWDRVGILIVLLVLLILMSTFAPNFNRV--------DNLLNIARSISVNAILAAGMTFV 71 Query: 77 IATGGIDLSVGAVMAIAGATTAAMTVAGFSLPIVLLSALGTGILAGLWNGILVAILKIQP 136 I T GIDLSVG+++A++G + +AG P+ +L+ +G G L GL NG+L A L + P Sbjct: 72 ILTSGIDLSVGSIVAVSGVVSVVAAMAGIPAPLAILAGVGVGALCGLLNGVLTAYLALAP 131 Query: 137 FVATLILMVAGRGVAQLITAGQIVTFNSPDLSWFGSGSLLFLPTPVIIAVLTLILFWLLT 196 F+ TL M RG+A IT GQ + +S G+G L+ +P PVII ++ +L W + Sbjct: 132 FIVTLGTMTFLRGMAYTITEGQPIVSSSLSFRELGNGYLIGIPIPVIIMLVVYLLAWFIL 191 Query: 197 RKTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGADANNA 256 +T G I AVG N +AA+ AGV + ++ Y+++G+CA +AGII AA + A A Sbjct: 192 ERTRFGRHIYAVGGNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVISAQP-TA 250 Query: 257 GLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPPEMNQVVKAVV 316 G ELDAI AVV+GG SL GGR ++ +++G++I+ ++TG++L P ++K +V Sbjct: 251 GTGYELDAIAAVVLGGTSLAGGRGRIIGTLIGSIILGVLSTGLILLSVPFFTQLLIKGIV 310 Query: 317 VLCVLIV 323 ++ + + Sbjct: 311 IILAVAI 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: 321 Number of extensions: 13 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 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