Align Galactose-proton symporter; Galactose transporter (characterized)
to candidate WP_066329840.1 BLR17_RS08985 sugar porter family MFS transporter
Query= SwissProt::P0AEP1 (464 letters) >NCBI__GCF_900100165.1:WP_066329840.1 Length = 452 Score = 233 bits (595), Expect = 8e-66 Identities = 142/437 (32%), Positives = 237/437 (54%), Gaps = 21/437 (4%) Query: 22 AALAGLLFGLDIGVIAGALPFIADEFQITSHTQEW-----VVSSMMFGAAVGAVGSGWLS 76 AALAG LFG D VI+GA + Q+ H+ + V++ ++G +GA+ + Sbjct: 11 AALAGFLFGFDTVVISGA----DKQLQLLWHSSDAFHGLIVMAMALWGTVIGAIFGAIPT 66 Query: 77 FKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAVGVASYTAPLYLSEIAPE 136 KLGRKK+L IL+ ++ +A A + V R + GL VG ++ AP Y+SEIAP Sbjct: 67 NKLGRKKTLFWIGILYFVSAIGAAFANDPYVFAAFRFIGGLGVGASTIAAPAYVSEIAPA 126 Query: 137 KIRGSMISMYQLMITIGILGAYLSDTAFSYTG--AWRWMLGVIIIPAILLLIGVFFLPDS 194 RG ++++YQ I +GIL A++S+ G AWRWM+GV IP+++ ++ + +P+S Sbjct: 127 DKRGRLVALYQFNIVLGILIAFISNYFLKDIGENAWRWMIGVQAIPSLIYILFIITIPES 186 Query: 195 PRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESLQVKQSGWALFKENSNFRRAVFL 254 PRW ++ R +A +VL + D A + +D+ RE+ K + K +R + L Sbjct: 187 PRWLLSRNRDTEAGKVLFEI-DPLASIEDLIDDSRENGVTKHENIFMKK----YRFPLML 241 Query: 255 GVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMWGTVIVGLTNVLATFIAIGLVDRW 314 L+ QF+G+N +YYAP+IFE AG T + ++ +G+TN++ T + + L+D+ Sbjct: 242 AFLMAFFNQFSGINAFLYYAPRIFEEAGLGQNT-ALLSSIGIGITNLIFTLVGVSLIDKL 300 Query: 315 GRKPTLTLGFLVMAAGMGVLGTMMHIGIHSPSAQYFAIAMLLMFIVGFAMSAGPLIWVLC 374 GRK + +G L +G++ + S F L +FI A+ G +IWV Sbjct: 301 GRKVLMYIGSLGYIISLGLVSASFYFNWGGLSVPVF----LFLFIASHAIGQGAVIWVFI 356 Query: 375 SEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNTLGNANTFWVYAALNVLFILLTLW 434 SEI P R G ++ +W+ I+ + + + +G + F ++ + VL +L ++ Sbjct: 357 SEIFPNHIRAAGQAFGSSVHWVLAAIIPSLIPMLFSEIGPSVVFLIFTLMMVLQLLFVMF 416 Query: 435 LVPETKHVSLEHIERNL 451 L+PETK +SLE + NL Sbjct: 417 LMPETKGISLETLSENL 433 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: 615 Number of extensions: 26 Number of successful extensions: 5 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: 452 Length adjustment: 33 Effective length of query: 431 Effective length of database: 419 Effective search space: 180589 Effective search space used: 180589 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: 51 (24.3 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