Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate BWI76_RS00280 BWI76_RS00280 ribose ABC transporter permease
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__Koxy:BWI76_RS00280 Length = 321 Score = 193 bits (490), Expect = 6e-54 Identities = 115/314 (36%), Positives = 184/314 (58%), Gaps = 13/314 (4%) Query: 18 WPTGMPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALLAIGMTLVI 77 W L+ALL+++ + S ++P+F+ V LF +IL + + A++A+GMTLVI Sbjct: 16 WLMEQKSLIALLVLIAIVSTMSPNFFTV----NNLF----NILQQTSVNAIMAVGMTLVI 67 Query: 78 ATGGIDLSVGAVMAIAGATTAAMTVAGFSLPIVLLSALGTGILAGLWNGILVAILKIQPF 137 T GIDLSVG+++A+ GA A++ + + + +AL G G G++VA ++Q F Sbjct: 68 LTSGIDLSVGSLLALTGAVAASIVGIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAF 127 Query: 138 VATLILMVAGRGVAQLITAGQIV----TFNSPDLSWFGSGSLLFLPTPVIIAVLTLILFW 193 +ATL++M+ RGV + T G V T N+ WFG G L +PTPV I + + W Sbjct: 128 IATLVMMLLLRGVTMVYTNGSPVNTGFTDNADLFGWFGIGRPLGIPTPVWIMAIVFLAAW 187 Query: 194 LLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGADA 253 + T LG +I A+G N A + +G++ + ++ Y L G+ A++AGII A + A Sbjct: 188 YMLHHTRLGRYIYALGGNEAATRLSGISVNKVKIIVYSLCGMLASLAGIIEVARLSSAQP 247 Query: 254 NNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPPEMNQVVK 313 AG ELDAI AVV+GG SL GG+ ++ +++GALI+ +N G+ L G +VK Sbjct: 248 -TAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVK 306 Query: 314 AVVVLCVLIVQSQR 327 AVV+L ++V +++ Sbjct: 307 AVVILLAVLVDNKK 320 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: 297 Number of extensions: 16 Number of successful extensions: 3 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: 321 Length adjustment: 28 Effective length of query: 313 Effective length of database: 293 Effective search space: 91709 Effective search space used: 91709 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