Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate GFF3462 PS417_17725 ribose ABC transporter permease
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__WCS417:GFF3462 Length = 330 Score = 179 bits (454), Expect = 9e-50 Identities = 109/315 (34%), Positives = 178/315 (56%), Gaps = 12/315 (3%) Query: 14 RRFRWPTGMPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPV-ALLAIG 72 R R P P V L++V LV ++ D L S + + R + A++A+G Sbjct: 25 RLVRSPAFYP-FVGLVVVTLV---------MILASDTFLTASNLSNIARQVSINAIIAVG 74 Query: 73 MTLVIATGGIDLSVGAVMAIAGATTAAMTVAGFSLPIVLLSALGTGILAGLWNGILVAIL 132 MT VI TGGIDLSVG VMA++G TA + VAG + + + + G+ G+ NG+ VA L Sbjct: 75 MTCVILTGGIDLSVGPVMALSGTLTAGLMVAGLPPGLAIGAGMLIGVAFGIGNGLFVAYL 134 Query: 133 KIQPFVATLILMVAGRGVAQLITAGQIVTFNSPDLSWFGSGSLLFLPTPVIIAVLTLILF 192 + P + TL M RG+ + T G ++ ++FG SL + P++I +LT ++ Sbjct: 135 HMPPIIVTLATMGIARGLGLMYTDGYPISGLPDWFAFFGRESLFGIQVPILIMLLTYLVA 194 Query: 193 WLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGAD 252 ++L + T +G +I A+G N A + +GV +L Y +SGL AAIAG+++ + + Sbjct: 195 YVLLQHTRIGRYIYAIGGNEEAVRLSGVRAARFKLLVYGISGLTAAIAGLVLTSRLMSGQ 254 Query: 253 ANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPPEMNQVV 312 NAG+ ELDAI AVV+GG S+ GGR ++ +++GA+++ +N G+ + G P + V+ Sbjct: 255 P-NAGVSFELDAIAAVVLGGASIAGGRGVIVGTLLGAMLLGVLNNGLNMLGVSPYVQSVI 313 Query: 313 KAVVVLCVLIVQSQR 327 K ++L + + QR Sbjct: 314 KGGIILLAIFISRQR 328 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: 313 Number of extensions: 15 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: 330 Length adjustment: 28 Effective length of query: 313 Effective length of database: 302 Effective search space: 94526 Effective search space used: 94526 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