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 CA265_RS23325 CA265_RS23325 MFS transporter
Query= TCDB::Q9LT15 (514 letters) >FitnessBrowser__Pedo557:CA265_RS23325 Length = 443 Score = 219 bits (559), Expect = 1e-61 Identities = 136/464 (29%), Positives = 231/464 (49%), Gaps = 35/464 (7%) Query: 22 TAFVIMTCIVAAMGGLLFGYDLGISGGVTSMEEFLTKFFPQVESQMKKAKHDTAYCKFDN 81 TA++ ++AA GG LFG+D + G P +E Q + + + Sbjct: 8 TAYITFISLLAAGGGYLFGFDFAVISGS----------LPFLEKQFQLTPYWEGFA---- 53 Query: 82 QMLQLFTSSLYLAALVASFMASVITRKHGRKVSMFIGGLAFLIGALFNAFAVNVSMLIIG 141 T SL L A+V +A ++ +GRK + I FL +L A A N I+ Sbjct: 54 ------TGSLALGAMVGCLIAGYVSDAYGRKPGLMIAAFVFLASSLAMAMAPNRDFFIVS 107 Query: 142 RLLLGVGVGFANQSTPVYLSEMAPAKIRGALNIGFQMAITIGILVANLINYGTSKMAQHG 201 R G+GVG A+ +P+Y++E+AP K RG L Q+ I +GIL+ NLINY + Sbjct: 108 RFFSGIGVGMASMLSPMYIAELAPPKFRGRLVAINQLTIVLGILITNLINYTLRNTGEDA 167 Query: 202 WRVSLGLAAVPAVVMVIGSFILPDTPNSMLERGKNEEAKQMLKKIRGADNVDHEFQDLID 261 WR GL A+P+ + +IG ILP++P ++++GKNE+A ++L KI + +++ Sbjct: 168 WRWMFGLGAIPSGIFLIGISILPESPRWLVQKGKNEKALKVLNKIGNHEFAADALKNIEQ 227 Query: 262 AVEAAKKVENPWKNIMESKYRPALIFCSAIPFFQQITGINVIMFYAPVLFKTLGFGDDAA 321 ++ VE+ ++I Y PA++ + FQQ GIN + YAP LF+++G D Sbjct: 228 TLQRKSNVEH--ESIFNKMYFPAVMIGIGLAIFQQFCGINTVFNYAPKLFESIGTSQDDQ 285 Query: 322 LMSAVITGVVNMLSTFVSIYAVDRYGRRLLFLEGGIQMFICQLLVGSFIGARFGTSGTGT 381 L+ V G VN++ T +++ VD+ GR+ L L G + + +L+ + SG+ Sbjct: 286 LLQTVFIGAVNVIFTISAMFLVDKIGRKPLMLIGAGGLAVLYVLISQLL-----ASGS-- 338 Query: 382 LTPATADWILAFICVYVAGFAWSWGPLGWLVPSEICPLEIRPAGQAINVSVNMFFTFLIG 441 W F+ + +A S P+ W++ SEI P ++R + F++ Sbjct: 339 ---TMVSW---FLLSAIGVYAVSLAPVTWVLISEIFPNKVRVKATTWAILCLWGAYFVLV 392 Query: 442 QFFLTMLCHMKFGLFYFFASMVAIMTVFIYFLLPETKGVPIEEM 485 F + +K +FY +A++ + + I+ + ETKG +EE+ Sbjct: 393 FTFPILFDWLKESIFYIYAAICTLGCIGIWKFVKETKGKTLEEI 436 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: 598 Number of extensions: 33 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: 514 Length of database: 443 Length adjustment: 33 Effective length of query: 481 Effective length of database: 410 Effective search space: 197210 Effective search space used: 197210 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: 51 (24.3 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