Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate N515DRAFT_3233 N515DRAFT_3233 xylose ABC transporter membrane protein
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__Dyella79:N515DRAFT_3233 Length = 380 Score = 159 bits (401), Expect = 1e-43 Identities = 121/366 (33%), Positives = 188/366 (51%), Gaps = 65/366 (17%) Query: 10 FRELGPLVALVSLAVFTAILNPR-FLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAID 68 ++ L L+A+ ++ VF + F+TA N+ L RQ+AI G+LA G FVII+G ID Sbjct: 13 YKILALLLAVAAIWVFFHVATGGDFVTARNVSNLFRQMAITGMLACGMVFVIIAG--EID 70 Query: 69 LSPGSMVALTGVMVAWLMTH---GVPV------------------WISVILILLFSIGAG 107 LS GS++ L G +VA L + PV W++ + + F +G G Sbjct: 71 LSVGSLLGLLGGVVAVLTVNQGWSTPVAIVAVLGLGVLIGLFNGFWVTRLRVPSFIVGLG 130 Query: 108 ---AWHGLFV------TKLRVPAFIITLG--------TLTIARGMAAVITKGWPIIGLPS 150 A+ G+ + T VPA ++ LG + + + AV+ + Sbjct: 131 GMLAFRGVLLGTTHSATIAPVPADLVYLGQGYVSPLWSTVLGVAIFAVVVALAVLRRRRR 190 Query: 151 SFLKIGQ----GEFLK--------------------IPIPVWILLAVALVADFFLRKTVY 186 + L+I Q + LK IP+PV IL+A+ V + +TV Sbjct: 191 AQLQIRQLPWWADLLKVVAIGAALGVFVATLNSYGGIPLPVLILVALLAVFSYLASQTVL 250 Query: 187 GKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYEL 246 G+H+ A GGN A R SGVNV RV+++ F + G + GI+ ARL+ G P G+ EL Sbjct: 251 GRHIYAVGGNLEATRLSGVNVARVKLVVFGIMGLMCAFAGIVNTARLAAGSPSAGTNGEL 310 Query: 247 YAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVT 306 AIA+ IGG S+ GG G+V GA++GA +++ L N + +++V TYW +V G ++V+AV Sbjct: 311 DAIAACFIGGASMRGGAGTVHGALIGALVMASLDNGMSMMDVDTYWQYIVKGAILVLAVW 370 Query: 307 LDILRR 312 +D+L R Sbjct: 371 VDVLSR 376 Lambda K H 0.328 0.143 0.424 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: 407 Number of extensions: 32 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 317 Length of database: 380 Length adjustment: 29 Effective length of query: 288 Effective length of database: 351 Effective search space: 101088 Effective search space used: 101088 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: 49 (23.5 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