Align Glucose/fructose transport protein (characterized, see rationale)
to candidate WP_086511015.1 BZY95_RS16640 MFS transporter
Query= uniprot:A0A0H3C6H3 (478 letters) >NCBI__GCF_002151265.1:WP_086511015.1 Length = 468 Score = 569 bits (1467), Expect = e-167 Identities = 275/454 (60%), Positives = 353/454 (77%), Gaps = 1/454 (0%) Query: 24 FVAAIVAVATIGGFMFGYDSGVINGTQEGLESAFNLSKLGTGLNVGAILIGCAIGAFAAG 83 ++ I +A IGGF+FG+DSGVINGT +GL++AF +GTG NV ++L+GCA+GAF AG Sbjct: 12 YIFMICCIAAIGGFLFGFDSGVINGTVDGLQAAFGSDSVGTGFNVASMLLGCAVGAFFAG 71 Query: 84 RLADVWGRRTVMIISALLFVISAIGTGAAESSIVFIIFRLIGGLGVGAASVLCPVYISEV 143 RLAD +GRRT++I++A+LF++SA G+G A SS+ F+ +R++GG+ VGAASV+ P YISEV Sbjct: 72 RLADRFGRRTLLIVAAILFLVSAWGSGVAGSSLEFVFYRVLGGMAVGAASVMTPAYISEV 131 Query: 144 TPANIRGRLSSVQQIMIITGLTGAFVANYALAHTAGSSTAEFWLGLPAWRWMFWMQIIPA 203 PA RGRL+++QQ+ II+GL AF++NY LAH +GS+ AE WLG WRWMFW++++PA Sbjct: 132 APAAYRGRLATIQQVAIISGLFVAFLSNYVLAHVSGSAMAELWLGFATWRWMFWIELLPA 191 Query: 204 GVFFLCLLGIPESPRYLVAKGKDAQAEAILSRLFGAGQGAKKVEEIRASLSADHKPTFSD 263 VF L LL IPESPRYL++ GK +A +L + G+ + K+ EI A+L+ DHKP D Sbjct: 192 TVFLLALLFIPESPRYLISSGKQGEARRVLGLVMPEGEVSAKMAEIDATLARDHKPRLRD 251 Query: 264 LLDPTTKKLRVILWAGLVLAVFQQLVGINIVFYYGSVLWQSVGFTEDDSLKINILSGTLS 323 +LD TT K+ I+W G+ LAVFQQLVGIN+VFYYG+VLWQSVGF+E D+L IN++SG +S Sbjct: 252 VLDRTTGKVHGIVWVGIGLAVFQQLVGINVVFYYGAVLWQSVGFSEGDALLINVISGAVS 311 Query: 324 ILACLLAIGLIDKIGRKPLLLIGSAGMAVTLGVLTWCFSTATTVNGALTLGDQIGLTALI 383 I ACLLAI LIDKIGRKPLL GS GMA+TL + + FSTAT ++G L LGD +G+ AL+ Sbjct: 312 IGACLLAIALIDKIGRKPLLWAGSVGMALTLACMAFAFSTATLIDGRLRLGDDMGVLALL 371 Query: 384 AANLYVIFFNLSWGPVMWVMLGEMFPNQMRGSALAVCGFAQWIANFAISVSFP-ALAAAS 442 AAN YV FFN+SWGPVMWVMLGEMFPNQMRGS LA+ G QW+ANF I+++FP LA Sbjct: 372 AANAYVFFFNVSWGPVMWVMLGEMFPNQMRGSGLAIAGLFQWLANFGITMTFPIMLATIG 431 Query: 443 LPMTYGFYALSAVVSFFLVQKLVHETRGKELEAM 476 L YGFYAL AVVS F V +LV ETRGKELE M Sbjct: 432 LAGAYGFYALCAVVSVFFVLRLVKETRGKELEEM 465 Lambda K H 0.325 0.138 0.417 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: 758 Number of extensions: 33 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: 478 Length of database: 468 Length adjustment: 33 Effective length of query: 445 Effective length of database: 435 Effective search space: 193575 Effective search space used: 193575 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