Align D-xylose-proton symporter (characterized)
to candidate BWI76_RS21205 BWI76_RS21205 MFS transporter
Query= CharProtDB::CH_109760 (491 letters) >FitnessBrowser__Koxy:BWI76_RS21205 Length = 478 Score = 323 bits (827), Expect = 1e-92 Identities = 183/485 (37%), Positives = 281/485 (57%), Gaps = 43/485 (8%) Query: 3 TQYNSSYIFSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVA 62 T Y+++I LVA GGLLFGYD VI G F ++++ A + G+ ++ Sbjct: 6 THLKMGYVWTICLVAACGGLLFGYDWVVIGGAKPFYEAWF----SITDPAQS---GWAMS 58 Query: 63 SALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYL 122 SAL+GC+ G + G+C+++ GR+ L ++AVLF S G+A + Sbjct: 59 SALVGCVFGALISGWCADKLGRKLPLILSAVLFSASAWGTA------------------V 100 Query: 123 AGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVN 182 A FV+YRI+GG+G+GLAS LSP+YIAE++PA RG+ V+ NQ I+ G L +N Sbjct: 101 ASSFDMFVVYRIVGGVGIGLASALSPLYIAEVSPAEKRGRFVAVNQLTIVIGVLAAQLIN 160 Query: 183 YFIARSGDA---------SWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQ 233 IA +W GWR+MF +E +PAL FL+L++ VPESPRWLM GK Sbjct: 161 LMIAEPVATGATQQMIVETWNGQMGWRWMFGAELVPALAFLVLMFFVPESPRWLMKAGKP 220 Query: 234 EQAEGILRKIMGNTLATQAVQEIKHSL--DHGRKTGGRLLMFGVG-VIVIGVMLSIFQQF 290 E+A L +I A + +++I H+L D+ + + G LL V +++IG++L++FQQ+ Sbjct: 221 ERARAALERIGSADYADRILRDIAHTLEKDNHKVSYGALLAPQVKPIVIIGMVLAVFQQW 280 Query: 291 VGINVVLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGAL 350 GINV+ YA E+F + G + L + GV+NL FT+ A+ VDK GR+ L ++GA Sbjct: 281 CGINVIFNYAQEIFASAGFDINSTLKSIVATGVVNLVFTLAALPLVDKIGRRKLMLLGAS 340 Query: 351 GMAIGMFSLGTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAI 410 G+ + + A+ G LL +L +A +A++ PV WVLL+EIFPN +RG A+++ Sbjct: 341 GLTLIYVLIAGAYAMGIMGWPVLLLVLAAIAIYALTLAPVTWVLLAEIFPNRVRGLAMSL 400 Query: 411 AVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKT 470 A W+A + +++TFP+++ A S+ +YG + L++ + VPETKG T Sbjct: 401 GTLALWIACFLLTYTFPLLN------AGLGAAGSFLLYGVICAAGYLYILRNVPETKGVT 454 Query: 471 LEELE 475 LE LE Sbjct: 455 LEALE 459 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: 621 Number of extensions: 28 Number of successful extensions: 6 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: 478 Length adjustment: 34 Effective length of query: 457 Effective length of database: 444 Effective search space: 202908 Effective search space used: 202908 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