Align ABC transporter for Xylitol, permease component 1 (characterized)
to candidate AO353_25120 AO353_25120 ABC transporter permease
Query= reanno::Dino:3607126 (288 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25120 Length = 320 Score = 140 bits (353), Expect = 4e-38 Identities = 94/289 (32%), Positives = 149/289 (51%), Gaps = 21/289 (7%) Query: 8 KTVFAFIGPAVIGLALVGIAPLLYALWTSLHFYNLTKLRRVEFIGLENY-------WT-V 59 + + F+ P ++ LALV PLL W SL NL F+GL NY W+ + Sbjct: 27 RAAWLFLTPMLLCLALVAAWPLLRTFWFSLTDANLADTSGGSFVGLSNYLFHDGSNWSGI 86 Query: 60 LTDEVFWQAMGRTFFLLGTALPLQIALGLGIALVLHQP--GLTLVKTLARLSLVLPMATT 117 L D +W A+ T ++ L+I LGL +AL+L+ G +LV+ L +++P A Sbjct: 87 LVDPQWWNAVRNTLHFTVVSVGLEIVLGLLVALLLNIKFTGRSLVRAL----ILIPWAIP 142 Query: 118 YAVVGLLGQVMFNQKFGVVNQL-----LGGADINWIGDPENAFAMIIFWDVWQWTPFVAL 172 V + M N +FG++N L L A + W D + + +I DVW+ PFV L Sbjct: 143 TIVSAKIWSWMLNDQFGIINHLMLSLGLIDAPLAWTADADLSMWAVIIVDVWKTVPFVTL 202 Query: 173 VLLAGLTMVPGEVEEAARLETKSKWTVLRYVQLPFLLPGLVAVLILRTADTLKLFDMVFT 232 ++LA L M+P + EAAR++ V V LP L+P L+ I R D+L++FD+++ Sbjct: 203 LMLAALQMLPSDCYEAARVDGIHPLKVFWRVTLPLLMPALLVAAIFRILDSLRVFDVIYV 262 Query: 233 LTRGGPGSSTEFISLMIQRVGFRGFDQGLASAQAIILLIITIVLAQIYI 281 LT SST +S+ ++ D G SA + +L ++ V+A +Y+ Sbjct: 263 LTSN--SSSTMSMSVYARQHLVEFQDVGYGSAASTLLFLVVAVIAMLYL 309 Lambda K H 0.329 0.144 0.440 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: 277 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: 288 Length of database: 320 Length adjustment: 27 Effective length of query: 261 Effective length of database: 293 Effective search space: 76473 Effective search space used: 76473 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 (21.8 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