Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate WP_078430749.1 BK574_RS01735 ABC transporter permease
Query= TCDB::Q9WXW7 (317 letters) >NCBI__GCF_002019605.1:WP_078430749.1 Length = 321 Score = 157 bits (397), Expect = 3e-43 Identities = 91/301 (30%), Positives = 162/301 (53%), Gaps = 4/301 (1%) Query: 7 KRTFRELGPLVALVSLAVFTAILNPRFLTAF-NLQALGRQIAIFGLLAIGETFVIISGGG 65 K G ++A + + + +IL+P +F N + RQI+ ++A+G T V+ Sbjct: 13 KSLISSYGTIIAGLGIIIIFSILSPSSFASFDNFINITRQISFLVIIALGATLVMAVK-- 70 Query: 66 AIDLSPGSMVALTGVMVAWLMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFIIT 125 DLS G+M +L GV+ A L G P+ +++ ++ G ++G VTK +V +F+ T Sbjct: 71 EFDLSIGAMASLGGVLSALLAASGTPIIFCLLVPIIVGFVVGFFNGAIVTKFKVLSFVTT 130 Query: 126 LGTLTIARGMAAVITKGWPII-GLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRKT 184 L T+ G+ +T G + +P F +GQ + +P I+ + ++ + + +T Sbjct: 131 LAMGTVIGGVTFWLTGGATVFENIPEGFKFLGQSKLAFLPTLSVIMFVLVIIFWYIMSQT 190 Query: 185 VYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMY 244 G+ L A GGNE A+ SG+N+ R + IAF + G LA G ++A+RL P G + Sbjct: 191 SLGRRLYAIGGNEKASEVSGINIARYKNIAFALCGMLAAFTGALLASRLGSAHPTGGDGF 250 Query: 245 ELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVA 304 L A A+ +G T + G ++LG + GA+II ++ N L +L V ++ N++ G +I++A Sbjct: 251 FLNAYAAVFLGMTIVKNGVPNILGTLFGAAIIGIMANGLTILEVPSFIQNIITGAIIIIA 310 Query: 305 V 305 + Sbjct: 311 L 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: 316 Number of extensions: 27 Number of successful extensions: 3 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: 321 Length adjustment: 28 Effective length of query: 289 Effective length of database: 293 Effective search space: 84677 Effective search space used: 84677 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 Apr 09 2024. 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