Align glucose transporter, periplasmic substrate-binding component (characterized)
to candidate WP_007680677.1 BN137_RS01920 D-xylose ABC transporter substrate-binding protein
Query= reanno::Phaeo:GFF3639 (341 letters) >NCBI__GCF_000319285.1:WP_007680677.1 Length = 330 Score = 233 bits (594), Expect = 5e-66 Identities = 127/318 (39%), Positives = 191/318 (60%), Gaps = 7/318 (2%) Query: 15 TASMAFAEDVTVGVSWSNFQEERWKTDEAAIKAALEAKGATYVSADAQSSSAKQLSDIES 74 T+ A+DV +G++ + + ERW+ D + E+ GA A + Q+S IE+ Sbjct: 17 TSFSGIAKDVKIGMAIDDLRLERWQKDRDIFVSKAESLGAKVFVQSANGNEETQMSQIEN 76 Query: 75 LIAQGVDALIVLAQDAQAIGPAVQAAADEGIPVVAYDRLIEDGRA-FYLTFDNVEVGRMQ 133 +I +GVD L+++ + Q + + A EGI V+AYDR+I + FY++FDN +VG +Q Sbjct: 77 MINRGVDVLVIIPYNGQVLSNVIAEAKREGIKVLAYDRMINNADIDFYISFDNEKVGEIQ 136 Query: 134 ARAVLEAQPSGNYVMIKGSPTDPNADFLRGGQQEIIQAAIDSGDIKIVGEAYTDGWLPAN 193 A+++++ P GNY ++ GSP D NA R GQ ++++ IDSG IK+VG+ + DGWLP N Sbjct: 137 AQSLVDNVPQGNYFLMGGSPVDNNARLFRDGQMKVLKPFIDSGKIKVVGDQWVDGWLPEN 196 Query: 194 AQRNMEQILTANDNKVDAVVASNDGTAGGVVAALTAQGMEG-IAVSGQDGDHAALNRVAK 252 A + ME LTAN+NK+DAVVASND TAGG + AL+AQG+ +A+SGQD D A + R+ Sbjct: 197 ALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLASKVAISGQDADLAGIKRIMA 256 Query: 253 GTQTVSVWKDARDLGKAAANIAVEMAEGAVMGDVAGGAAWTSPAGTELTARFLEPIPVTA 312 GTQT++V+K L AA +AVE+ A + ++ +R L PI V Sbjct: 257 GTQTMTVYKPITQLANTAAEVAVELGN----DKQPKSDATLNNGLKDVPSRLLTPIKVDK 312 Query: 313 DNL-SVVVDAGWITKEAL 329 N+ S V+ G+ K L Sbjct: 313 SNIESTVIKDGFHKKSDL 330 Lambda K H 0.313 0.128 0.362 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: 232 Number of extensions: 9 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: 341 Length of database: 330 Length adjustment: 28 Effective length of query: 313 Effective length of database: 302 Effective search space: 94526 Effective search space used: 94526 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 24 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