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 N515DRAFT_1228 N515DRAFT_1228 MFS transporter, SP family, galactose:H+ symporter
Query= TCDB::Q9LT15 (514 letters) >FitnessBrowser__Dyella79:N515DRAFT_1228 Length = 463 Score = 243 bits (621), Expect = 8e-69 Identities = 150/471 (31%), Positives = 256/471 (54%), Gaps = 37/471 (7%) Query: 21 VTAFVIMTCIVAAMGGLLFGYDLGISGGVTSMEEFLTKFFPQVESQMKKAKHDTAYCKFD 80 V VI TC++AA+ GL+FG D+G+ G SQ KA+ Sbjct: 13 VKGTVIYTCVLAALAGLMFGLDIGVISGA---------------SQFIKAEF-----AIS 52 Query: 81 NQMLQLFTSSLYLAALVASFMASVITRKHGRKVSMFIGGLAFLIGALFNAFAVNVSMLII 140 + ++ SS+ A V + A ++ GRK S+ +G + F+IG+L A + LI Sbjct: 53 DHTIEWIVSSMMFGAAVGALGAGWLSSHLGRKRSLILGAILFVIGSLLCGLAWSPETLIA 112 Query: 141 GRLLLGVGVGFANQSTPVYLSEMAPAKIRGALNIGFQMAITIGILVANLINYGTSKMAQH 200 R++LG+ +G A + P+YL+E+AP IRGA+ +Q+ ITIGILVA L + ++ H Sbjct: 113 ARVILGLAIGIATFTAPLYLAEVAPEHIRGAMISTYQLMITIGILVAFL---SDTALSYH 169 Query: 201 G-WRVSLGLAAVPAVVMVIGSFILPDTPNSMLERGKNEEAKQMLKKIRGADNVDHEFQDL 259 G WR LG+ A+P + ++G LPD+P ++ RG+ +EA +L+++RG + V ++ Sbjct: 170 GAWRWMLGVIAIPGALFLLGVLGLPDSPRWLMMRGRRDEAIDVLRRLRGDEVV--VAREA 227 Query: 260 IDAVEAAKKVENPWKNIMES-KYRPALIFCSAIPFFQQITGINVIMFYAPVLFKTLGFGD 318 D E K + W E+ +R ++ + + QQ TG+NV+M+YAP +F+ +G+ Sbjct: 228 ADIEEQLKTPQRGWDLFAENPNFRRSVFLGALLQIMQQFTGMNVVMYYAPRIFQEMGYDT 287 Query: 319 DAALMSAVITGVVNMLSTFVSIYAVDRYGRRLLFLEGGIQMFICQLLVGSFIGARFGTSG 378 A + + G+ N+L+TF++I +DR+GR+ + G M + +VG+ + Sbjct: 288 AAQMWFTALVGLTNVLATFIAIALIDRWGRKPILYTGFAVMAVGLGVVGALM-------- 339 Query: 379 TGTLTPATADW-ILAFICVYVAGFAWSWGPLGWLVPSEICPLEIRPAGQAINVSVNMFFT 437 G + T + +A + ++ GFA S GPL W + SEI PL+ R G ++ N Sbjct: 340 NGGINGQTEQYTCVAMLLFFIVGFAMSAGPLVWTLCSEIQPLKGRDFGIGVSTFTNWITN 399 Query: 438 FLIGQFFLTMLCHM-KFGLFYFFASMVAIMTVFIYFLLPETKGVPIEEMGR 487 ++G FL++L + F+ +A++ A+ V ++L+PETKGV +E++ R Sbjct: 400 MVVGFTFLSLLNTIGNASTFWLYAALNAVFIVLTFWLVPETKGVTLEQIER 450 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: 633 Number of extensions: 30 Number of successful extensions: 7 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: 463 Length adjustment: 34 Effective length of query: 480 Effective length of database: 429 Effective search space: 205920 Effective search space used: 205920 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 Sep 17 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