Align Galactose-proton symporter; Galactose transporter (characterized)
to candidate WP_010537714.1 KCY_RS0114120 MFS transporter
Query= SwissProt::P0AEP1 (464 letters) >NCBI__GCF_000226135.1:WP_010537714.1 Length = 309 Score = 195 bits (496), Expect = 2e-54 Identities = 108/306 (35%), Positives = 178/306 (58%), Gaps = 21/306 (6%) Query: 11 NKAMTFFVCFLAALAGLLFGLDIGVIAGALPFIADEFQITSHTQEWVVSSMMFGAAVGAV 70 N + F+ +AAL G LFG D VI+G + ++ FQ+ + Q W V + G+ VG + Sbjct: 6 NFSYLIFLSVVAALGGFLFGYDTAVISGTIAQVSQLFQLDALQQGWYVGCALIGSIVGVL 65 Query: 71 GSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAVGVASYTAPLYL 130 +G LS KLGRK +++I A+LF +L A + + L++ R++ G+ +GV S +PLY+ Sbjct: 66 FAGILSDKLGRKLTMVISAVLFSTSALGCAISADFTQLVIYRIIGGVGIGVVSIVSPLYI 125 Query: 131 SEIAPEKIRGSMISMYQLMITIGILGAYLSD------------------TAFSYTGAWRW 172 SE++ + RG ++S+YQL +T+G LGAYL + T WR Sbjct: 126 SEVSVAQYRGRLVSLYQLAVTVGFLGAYLVNYQLLGYAQSGSQLSIDWLNKIFVTEVWRG 185 Query: 173 MLGVIIIPAILLLIGVFFLPDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESL 232 MLG+ ++PA+L I +FF+P+SPRW K + A +L ++ ++ +EA +L+E + L Sbjct: 186 MLGMEMLPAVLFFIIIFFIPESPRWLIVKGKEEKAVNILEKIYNSVSEATSQLNETKSVL 245 Query: 233 QVK-QSGWALFKENSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMW 291 + +S WAL + F +AV +GV + ++ QF G+N ++YY P IFE AG + + ++ Sbjct: 246 TSETKSEWALLMKPGIF-KAVIIGVCIAILGQFMGVNAVLYYGPSIFENAGLSG-GDSLF 303 Query: 292 GTVIVG 297 V+VG Sbjct: 304 YQVLVG 309 Lambda K H 0.327 0.140 0.425 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: 410 Number of extensions: 19 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: 464 Length of database: 309 Length adjustment: 30 Effective length of query: 434 Effective length of database: 279 Effective search space: 121086 Effective search space used: 121086 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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