Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate WP_066323743.1 BLR17_RS10195 sugar porter family MFS transporter
Query= TCDB::P15729 (468 letters) >NCBI__GCF_900100165.1:WP_066323743.1 Length = 465 Score = 298 bits (762), Expect = 3e-85 Identities = 177/466 (37%), Positives = 280/466 (60%), Gaps = 25/466 (5%) Query: 13 NVKFVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQ--TDSLLTGLSVSLALLGSALG 70 N ++L IS V+ALGG LFG+D VI GA ++ F T + L ++S AL+G LG Sbjct: 9 NNNYLLAISMVSALGGLLFGYDWVVIGGAKPFYERFFDITTSANLQAWAMSSALIGCILG 68 Query: 71 AFGAGPIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVIAPA 130 A +G I+D+ GR ++L+A LFT++S+G+GL W F+ +R++GG+G+G AS ++P Sbjct: 69 AVVSGVISDKFGRKWPLLLSAFLFTVASLGTGLASAYWIFVVFRIVGGVGIGLASALSPM 128 Query: 131 YIAEVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFIA--LMAGGS---AQNPWLFGAAAW 185 YIAEV+P+HLRGR +L Q+ +V GI A + N IA + AG S ++ W G W Sbjct: 129 YIAEVAPSHLRGRFVALNQMTLVVGILAAQIVNLLIADKVPAGVSDAFIRSSW-NGQMGW 187 Query: 186 RWMFWTELIPALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEGGDVPSRIEEIQATV 245 RWMF+ +P++++ + F +PESPR+L+ G+ +KA L K+ GG+V + E Sbjct: 188 RWMFFACAVPSVVFFLLVFTLPESPRWLMKAGKADKAFPTLQKI-GGEVYAHEEMANIKA 246 Query: 246 SLD---HKPRFSDLLSRRGGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRSVGFTEEK 302 +LD K F L + + ++ IG+ ++ QQ+ GIN +F Y+ ++ + G+ Sbjct: 247 TLDDVTEKIDFKALFNPK--FKDVLVIGIVIAVFQQWCGINTVFNYAEEIFTAAGYGVSD 304 Query: 303 SLLITVITGFINILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGATVVNGQP 362 +L VITG +N++ TLVA+ VDK+GRK L++ G++G+TIT +L F Sbjct: 305 TLFNIVITGTVNLIFTLVAMFTVDKWGRKKLMVFGALGLTITYLLLGSAF--------YF 356 Query: 363 TLTGAAGIIALVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFII 422 L G A +++LV + V++ S PI WV+L E+F N++R AA+++A W+A FI+ Sbjct: 357 DLKGVA-VLSLVVIAIAVYA--MSLAPITWVILSEIFPNRVRGAAMALATFALWVACFIL 413 Query: 423 STTFPPLLDTVGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468 + TFP L T+G + +YA + F+ + ETKGKTLE++ Sbjct: 414 TYTFPLLNKTLGAAGTFWVYAGICVLGFLFVLIRLPETKGKTLEEI 459 Lambda K H 0.325 0.140 0.430 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: 551 Number of extensions: 31 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: 468 Length of database: 465 Length adjustment: 33 Effective length of query: 435 Effective length of database: 432 Effective search space: 187920 Effective search space used: 187920 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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