Align The high affinity sugar:H+ symporter (sugar uptake) porter of 514 aas and 12 TMSs, STP10. It transports glucose, galactose and mannose, and is therefore a hexose transporter (Rottmann et al. 2016). The 2.4 (characterized)
to candidate BWI76_RS24055 BWI76_RS24055 MFS transporter
Query= TCDB::Q9LT15 (514 letters) >FitnessBrowser__Koxy:BWI76_RS24055 Length = 464 Score = 234 bits (598), Expect = 4e-66 Identities = 153/463 (33%), Positives = 251/463 (54%), Gaps = 36/463 (7%) Query: 29 CIVAAMGGLLFGYDLGISGGVTSMEEFLTKFFPQVESQMKKAKHDTAYCKFDNQMLQLFT 88 C +AA+ GLLFG D+G+ G P + ++ + + H + Sbjct: 19 CFLAALAGLLFGLDIGVIAGA----------LPFIANEFQISAHTQEWV----------V 58 Query: 89 SSLYLAALVASFMASVITRKHGRKVSMFIGGLAFLIGALFNAFAVNVSMLIIGRLLLGVG 148 SS+ A V + + ++ K GRK S+ IG + F+ G+LF+A A NV +L+I R+LLG+ Sbjct: 59 SSMMFGAAVGAVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLLISRVLLGLA 118 Query: 149 VGFANQSTPVYLSEMAPAKIRGALNIGFQMAITIGILVANLINYGTSKMAQHGWRVSLGL 208 VG A+ + P+YLSE+AP KIRG++ +Q+ ITIGIL A L + T+ WR LG+ Sbjct: 119 VGVASYTAPLYLSEIAPEKIRGSMISMYQLMITIGILGAYLSD--TAFSYSGAWRWMLGV 176 Query: 209 AAVPAVVMVIGSFILPDTPNSMLERGKNEEAKQMLKKIRGADNVDHEFQDLIDAVEAAKK 268 +PAV+++IG LPD+P + + +A+++L ++R D ++L + E+ K Sbjct: 177 IIIPAVLLLIGVVFLPDSPRWFAAKRRFVDAERVLLRLR--DTSAEAKRELDEIRESLKV 234 Query: 269 VENPWKNIME-SKYRPALIFCSAIPFFQQITGINVIMFYAPVLFKTLGFGDDAALM-SAV 326 ++ W E S +R A+ + QQ TG+NVIM+YAP +F+ G+ + M V Sbjct: 235 KQSGWSLFKENSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYANTTEQMWGTV 294 Query: 327 ITGVVNMLSTFVSIYAVDRYGRRLLFLEGGIQMFICQLLVGSFIGARFGTSGTGTLTPAT 386 I G+ N+L+TF++I VDR+GR+ + G I M + ++GS + + AT Sbjct: 295 IVGLTNVLATFIAIGLVDRWGRKPTLILGFIVMALGMGILGSMMHI--------GIHSAT 346 Query: 387 ADWI-LAFICVYVAGFAWSWGPLGWLVPSEICPLEIRPAGQAINVSVNMFFTFLIGQFFL 445 A + + + +++ GFA S GPL W++ SEI PL+ R G + + N ++G FL Sbjct: 347 AQYFAVLMLLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFL 406 Query: 446 TMLCHM-KFGLFYFFASMVAIMTVFIYFLLPETKGVPIEEMGR 487 TML + F+ + + + +L+PETK V +E + R Sbjct: 407 TMLNSLGSANTFWVYGGLNILFIFLTLWLIPETKNVSLEHIER 449 Lambda K H 0.327 0.141 0.434 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: 621 Number of extensions: 24 Number of successful extensions: 8 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: 514 Length of database: 464 Length adjustment: 34 Effective length of query: 480 Effective length of database: 430 Effective search space: 206400 Effective search space used: 206400 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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