Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate Echvi_1280 Echvi_1280 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__Cola:Echvi_1280 Length = 318 Score = 241 bits (615), Expect = 2e-68 Identities = 133/304 (43%), Positives = 196/304 (64%), Gaps = 13/304 (4%) Query: 16 LVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLSPGSMV 75 L+AL+ L + ++L+ RFLT N + RQ+++ +++G T VI++ G IDLS GS++ Sbjct: 10 LIALIILCLVLSLLSDRFLTLANGWNVMRQVSVNICISVGMTLVILTAG--IDLSVGSIL 67 Query: 76 ALTGVMVAWLMTHGVPV-----------WISVILILLFSIGAGAWHGLFVTKLRVPAFII 124 AL G + A L+ +G+ V +VIL + G G ++G +T+ +VP F+ Sbjct: 68 ALCGAVTASLIKNGIAVEGLNLHIGFAPLGAVILGVGLGFGLGWFNGWTITRFKVPPFVA 127 Query: 125 TLGTLTIARGMAAVITKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRKT 184 TL LTIARG+ + T G+PI GL F +G G FL IP+PVWI + +A +KT Sbjct: 128 TLAMLTIARGLTMLWTGGFPINGLGEDFAFLGTGWFLGIPMPVWITAVIVALAVLLTKKT 187 Query: 185 VYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMY 244 +G+++ A GGNE AAR SG+N+ RV+M + ++G LA V G+I+ +RL QP G Y Sbjct: 188 KFGRYVYAIGGNERAARLSGINISRVKMTVYAIAGGLAAVGGMIVTSRLDSAQPNAGISY 247 Query: 245 ELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVA 304 EL AIA+ VIGGTSL+GG+G+++GA++G II +L N LVLLNVS +W VV G VI++A Sbjct: 248 ELDAIAAVVIGGTSLSGGKGTIMGAVLGGIIIGVLNNGLVLLNVSPFWQQVVKGAVILLA 307 Query: 305 VTLD 308 V +D Sbjct: 308 VVID 311 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: 357 Number of extensions: 19 Number of successful extensions: 4 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: 317 Length of database: 318 Length adjustment: 27 Effective length of query: 290 Effective length of database: 291 Effective search space: 84390 Effective search space used: 84390 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: 48 (23.1 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