Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate PP_2761 PP_2761 putative Ribose ABC transporter, permease protein
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__Putida:PP_2761 Length = 328 Score = 132 bits (333), Expect = 9e-36 Identities = 101/302 (33%), Positives = 158/302 (52%), Gaps = 11/302 (3%) Query: 22 MPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALLAIGMTLVIATGG 81 MP L A VLL +L AP F V G L +LN +A++AIGMT IA GG Sbjct: 26 MPTLFAA--VLLFFALKAPGFLTV----GNLSSL---LLNNFVLLAIVAIGMTYAIAAGG 76 Query: 82 IDLSVGAVMAIAGATTAAMTVAGFSLPIVLLSALGTGILAGLWNGILVAILKIQPFVATL 141 IDLSVG + + T + AGF L + + L G LAGL+N L+A L+I PF+ATL Sbjct: 77 IDLSVGTALDFSALTFVLLLNAGFGLYVAIPGGLLAGSLAGLFNAGLIAGLRISPFLATL 136 Query: 142 ILMVAGRGVAQLIT-AGQIVTFNSPDLSWFGSGSLLFLPTPVIIAVLTLILFWLLTRKTA 200 + G V +L++ GQ + + S + +L +P P+++ L +++ ++ + Sbjct: 137 GTLFIGSSVQKLLSEGGQPIYLEAQVRSGLATERMLGVPLPLLLVALLALVYGVVLARGR 196 Query: 201 LGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGADANNAGLWL 260 LG I +G A+ +G+ R I L ++ S +A+AGI++ A + A A +G Sbjct: 197 LGREIIVLGSQPLVARYSGLAQRRIAALVFIASAFASALAGILLPATV-NAYAPMSGNAF 255 Query: 261 ELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPPEMNQVVKAVVVLCV 320 ++AI AV IG + R N+ +++G L + G+LL G+ QV V++L V Sbjct: 256 LMNAIGAVFIGATLSLHNRVNVPGTLLGVLFLNVTANGLLLIGWNFFWQQVATGVLILSV 315 Query: 321 LI 322 L+ Sbjct: 316 LL 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: 295 Number of extensions: 28 Number of successful extensions: 2 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: 328 Length adjustment: 28 Effective length of query: 313 Effective length of database: 300 Effective search space: 93900 Effective search space used: 93900 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