Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate WP_057508163.1 ABB28_RS08195 MFS transporter
Query= TCDB::P15729 (468 letters) >NCBI__GCF_001431535.1:WP_057508163.1 Length = 474 Score = 452 bits (1164), Expect = e-132 Identities = 230/468 (49%), Positives = 324/468 (69%), Gaps = 4/468 (0%) Query: 4 SSSPSQSTANVKFVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSVSLA 63 S+S N F++LIS VA +GGFLFGFD+ VING V L+ F + G V+ Sbjct: 6 SASSGTQGENTAFIVLISCVATIGGFLFGFDSGVINGTVDGLRTAFNSSEAALGFEVASM 65 Query: 64 LLGSALGAFGAGPIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGA 123 LLG A+GAF AG + D GR +I++AVLF LS++G+G W F+ RV+GG VGA Sbjct: 66 LLGCAIGAFLAGRLGDLLGRRSVLIISAVLFLLSALGAGAAHASWLFVAARVIGGFAVGA 125 Query: 124 ASVIAPAYIAEVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFIALMAGGSAQNPWLFGAA 183 ASV+APAYIAEV+ A RG+L ++QQ+AI+SG+F A LSN+ +A AG S + WL G Sbjct: 126 ASVMAPAYIAEVASARYRGKLATVQQIAIISGLFAAFLSNYLLARAAGASTEVLWL-GQE 184 Query: 184 AWRWMFWTELIPALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEGG-DVPSRIEEIQ 242 AWRWMFW + IP+LL+ +IPESPR+LV +G+ +A+A+L ++ G + +++ EI+ Sbjct: 185 AWRWMFWMQAIPSLLFLALLLVIPESPRFLVVKGRRAEASAVLTRLYGAVEAQAKLGEIE 244 Query: 243 ATVSL-DHKPRFSDLLSRRGGLLP-IVWIGMGLSALQQFVGINVIFYYSSVLWRSVGFTE 300 +++ H+P F+DL + G L IVW+G+GL+ LQQ VGINV+FYY +VLW++VGF+E Sbjct: 245 HSLAQHQHRPSFADLKDKASGKLRGIVWVGIGLAVLQQLVGINVVFYYGAVLWQAVGFSE 304 Query: 301 EKSLLITVITGFINILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGATVVNG 360 +LLI V++G ++I LV + +D+ GRKPLL +GS+GM I L ++ V F ++V+G Sbjct: 305 NDALLINVLSGALSIGACLVTVVLIDRIGRKPLLWVGSVGMAIALALMVVAFSSGSLVDG 364 Query: 361 QPTLTGAAGIIALVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANF 420 + L+ G +ALV AN+YV F SWGP++WV+LGEMF N+IR +AL+VA QW +NF Sbjct: 365 RLQLSDGMGRLALVAANVYVVFFNMSWGPVMWVMLGEMFPNQIRGSALAVAGAAQWTSNF 424 Query: 421 IISTTFPPLLDTVGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468 I+ TFP LL +GL AY +YA +A +SIFF+ +V+ETKGK LEQM Sbjct: 425 AITVTFPILLAGIGLAGAYSIYAVAAFLSIFFVIRYVRETKGKELEQM 472 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: 635 Number of extensions: 24 Number of successful extensions: 4 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: 474 Length adjustment: 33 Effective length of query: 435 Effective length of database: 441 Effective search space: 191835 Effective search space used: 191835 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