Align D-xylose-proton symporter (characterized)
to candidate Ga0059261_1777 Ga0059261_1777 MFS transporter, sugar porter (SP) family
Query= CharProtDB::CH_109760 (491 letters) >FitnessBrowser__Korea:Ga0059261_1777 Length = 458 Score = 296 bits (757), Expect = 1e-84 Identities = 164/461 (35%), Positives = 260/461 (56%), Gaps = 41/461 (8%) Query: 17 ATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASALIGCIIGGALGG 76 A LGGLLFG+DTAVISG ++L F +++LGF VASALIG ++G + G Sbjct: 29 AALGGLLFGFDTAVISGATQALQLQF--------GLTDAMLGFTVASALIGTVLGSLIAG 80 Query: 77 YCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYVPEFVIYRIIG 136 ++RFGR+ + A+ + +S +G T + PD + F+++R +G Sbjct: 81 APADRFGRKGVMLTVAIAYVVSSLG--------TGLAPD----------LNAFLVFRFMG 122 Query: 137 GIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDASWLNT 196 G+ +G AS+++P+YIAE++PA RG+LV+ NQ I+ G L+ + NY IA + Sbjct: 123 GLAIGAASVVTPIYIAEVSPARFRGRLVAMNQLNIVLGILIAFLSNYIIA-----GLVQY 177 Query: 197 D-GWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKI-MGNTLATQAVQ 254 D WR+MF +P+ +FL++ +PESPRWL G+ ++A +++++ + A A Sbjct: 178 DVAWRWMFGIVAVPSTIFLLVTLLLPESPRWLAIHGQADRARDVMQRLGFADPRAELARI 237 Query: 255 EIKHSLDHGRKTGGRLLMFGVGVIVIGVMLSIFQQFVGINVVLYYAPEVFKTLGASTDIA 314 E+ + + + + +++F Q GIN +LYYAP +F+ GA D A Sbjct: 238 ELAEAREEAAGKPRLFQRSHFTPVACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSA 297 Query: 315 LLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFYTQAP-GIVAL 373 LLQ+I VG NL FTV A+ +D+FGR+PL +G++ A + +G + P G + L Sbjct: 298 LLQSIAVGGTNLVFTVAALFLIDRFGRRPLLFVGSVICAATLLLVGWQLESAKPDGTLIL 357 Query: 374 LSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNS 433 +L ++AAFAMS G V WV +SE+FP+A+RGK A+ W+ ++W FP+ Sbjct: 358 FGLLGFIAAFAMSQGAVIWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVF---- 413 Query: 434 WLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEEL 474 A G+ + +G M +L L+ WKF+PET G LE++ Sbjct: 414 ---AASVGGWVFAFFGAMMLLQLLWTWKFMPETNGIALEDM 451 Lambda K H 0.326 0.140 0.433 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: 636 Number of extensions: 34 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: 491 Length of database: 458 Length adjustment: 33 Effective length of query: 458 Effective length of database: 425 Effective search space: 194650 Effective search space used: 194650 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