Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate 17810 b3750 ribose ABC transporter permease protein (NCBI)
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__Keio:17810 Length = 321 Score = 194 bits (494), Expect = 2e-54 Identities = 120/325 (36%), Positives = 189/325 (58%), Gaps = 15/325 (4%) Query: 9 TTTPKRRFR--WPTGMPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPV 66 T + +R F W L+ALL+++ + S ++P+F+ + LF +IL + + Sbjct: 5 TVSGRRYFTKAWLMEQKSLIALLVLIAIVSTLSPNFFTI----NNLF----NILQQTSVN 56 Query: 67 ALLAIGMTLVIATGGIDLSVGAVMAIAGATTAAMTVAGFSLPIVLLSALGTGILAGLWNG 126 A++A+GMTLVI T GIDLSVG+++A+ GA A++ + + + +AL G G G Sbjct: 57 AIMAVGMTLVILTSGIDLSVGSLLALTGAVAASIVGIEVNALVAVAAALALGAAIGAVTG 116 Query: 127 ILVAILKIQPFVATLILMVAGRGVAQLITAGQIV----TFNSPDLSWFGSGSLLFLPTPV 182 ++VA ++Q F+ATL++M+ RGV + T G V T N+ WFG G L +PTPV Sbjct: 117 VIVAKGRVQAFIATLVMMLLLRGVTMVYTNGSPVNTGFTENADLFGWFGIGRPLGVPTPV 176 Query: 183 IIAVLTLILFWLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGI 242 I + + W + T LG +I A+G N A + +G+N I ++ Y L GL A++AGI Sbjct: 177 WIMGIVFLAAWYMLHHTRLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGI 236 Query: 243 IVAADIRGADANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLS 302 I A + A AG ELDAI AVV+GG SL GG+ ++ +++GALI+ +N G+ L Sbjct: 237 IEVARLSSAQP-TAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLL 295 Query: 303 GFPPEMNQVVKAVVVLCVLIVQSQR 327 G +VKAVV+L ++V +++ Sbjct: 296 GVSSYYQMIVKAVVILLAVLVDNKK 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: 301 Number of extensions: 18 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 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