Align D-xylose ABC transporter, periplasmic substrate-binding protein, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas (characterized)
to candidate GFF3639 PGA1_262p00430 D-xylose-binding periplasmic protein XylF
Query= TCDB::A6LW10 (359 letters) >FitnessBrowser__Phaeo:GFF3639 Length = 341 Score = 244 bits (622), Expect = 3e-69 Identities = 136/318 (42%), Positives = 194/318 (61%), Gaps = 6/318 (1%) Query: 23 LTGCGAKKDAQTSSNG-NKKIKIGVSMDDLRLERWQHDKEIFEEEAKKLGADVVFQSANG 81 L+G A A T+S + + +GVS + + ERW+ D+ + + GA V A Sbjct: 4 LSGVSALAFAATASMAFAEDVTVGVSWSNFQEERWKTDEAAIKAALEAKGATYVSADAQS 63 Query: 82 DDPTQMSQAENLISQGVDVLVVIPHNGESIAPIVEEAHQNKIKVLAYDRLITNSDLDYYV 141 Q+S E+LI+QGVD L+V+ + ++I P V+ A I V+AYDRLI + +Y+ Sbjct: 64 SSAKQLSDIESLIAQGVDALIVLAQDAQAIGPAVQAAADEGIPVVAYDRLIEDGRA-FYL 122 Query: 142 SFDNVKVGELQAKAIVDKTPKGNYFMMGGSPTDNNAKLFRQGQMNIIKPYVDKGDIKLVG 201 +FDNV+VG +QA+A+++ P GNY M+ GSPTD NA R GQ II+ +D GDIK+VG Sbjct: 123 TFDNVEVGRMQARAVLEAQPSGNYVMIKGSPTDPNADFLRGGQQEIIQAAIDSGDIKIVG 182 Query: 202 DQWVKDWSAEEALKIMENALTANNNKLDAVVASNDSTAGGAIQALQAQSLAGKITISGQD 261 + + W A + ME LTAN+NK+DAVVASND TAGG + AL AQ + G I +SGQD Sbjct: 183 EAYTDGWLPANAQRNMEQILTANDNKVDAVVASNDGTAGGVVAALTAQGMEG-IAVSGQD 241 Query: 262 ADLAGCQRVVEGTQTMTIYKPIKDIAAKAAEMAVKMAKGE---DVETGGTVTNNGKKDVP 318 D A RV +GTQT++++K +D+ AA +AV+MA+G DV G T+ ++ Sbjct: 242 GDHAALNRVAKGTQTVSVWKDARDLGKAAANIAVEMAEGAVMGDVAGGAAWTSPAGTELT 301 Query: 319 SVLLTPIAVTADNMKDTV 336 + L PI VTADN+ V Sbjct: 302 ARFLEPIPVTADNLSVVV 319 Lambda K H 0.312 0.130 0.360 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: 301 Number of extensions: 17 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: 359 Length of database: 341 Length adjustment: 29 Effective length of query: 330 Effective length of database: 312 Effective search space: 102960 Effective search space used: 102960 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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