Align glucose transporter, periplasmic substrate-binding component (characterized)
to candidate WP_008509253.1 BIBO1_RS15350 D-xylose ABC transporter substrate-binding protein
Query= reanno::Phaeo:GFF3639 (341 letters) >NCBI__GCF_000182725.1:WP_008509253.1 Length = 339 Score = 235 bits (600), Expect = 1e-66 Identities = 134/324 (41%), Positives = 190/324 (58%), Gaps = 12/324 (3%) Query: 11 AFAATASMAFAEDVTVGVSWSNFQEERWKTDEAAIKAALEAKGATYVSADAQSSSAKQLS 70 A AT + A E +G S + + ERW D AA E GA A + KQ+ Sbjct: 20 AMGATPASASPEHPVIGFSIDDLRVERWARDRDYFIAAAEKLGAKVNVQSADGNEEKQVK 79 Query: 71 DIESLIAQGVDALIVLAQDAQAIGPAVQAAADEGIPVVAYDRLIEDGRA-FYLTFDNVEV 129 +E+LI+QGVDA++++ +++ V A GI V++YDRLI + Y++FDN V Sbjct: 80 QVENLISQGVDAIVIVPMNSKVFDAVVADAKASGIKVLSYDRLILNADIDAYISFDNERV 139 Query: 130 GRMQARAVLEAQPSGNYVMIKGSPTDPNADFLRGGQQEIIQAAIDSGDIKIVGEAYTDGW 189 G MQA+AVL+A+P GNY ++ GSPTD NA LR GQ++ ++ A+DSG +KIVG + W Sbjct: 140 GFMQAQAVLKAKPEGNYYLLGGSPTDNNAKLLRAGQEKALKEAVDSGKVKIVGSQWVKEW 199 Query: 190 LPANAQRNMEQILTANDNKVDAVVASNDGTAGGVVAALTAQGMEG-IAVSGQDGDHAALN 248 P A ME LTA NK+DAVVASNDGTAGG + AL AQG+ G AVSGQD D AA+ Sbjct: 200 SPTEALSIMENALTATQNKIDAVVASNDGTAGGAIQALAAQGLAGKTAVSGQDSDLAAVK 259 Query: 249 RVAKGTQTVSVWKDARDLGKAAANIAVEMA---EGAVMGDVAGGAAWTSPAGTELTARFL 305 R+ GTQTV+V+K + + + AA + V++ + G + G+ ++ L Sbjct: 260 RLVDGTQTVTVYKPLKLIAEEAAKLTVQLVRDEKPEFNGKINNGS-------KDVDTLLL 312 Query: 306 EPIPVTADNLSVVVDAGWITKEAL 329 P VT DN+ + + G+ TKE + Sbjct: 313 TPTAVTKDNIDIYIKDGFYTKEQI 336 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: 247 Number of extensions: 12 Number of successful extensions: 5 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: 339 Length adjustment: 28 Effective length of query: 313 Effective length of database: 311 Effective search space: 97343 Effective search space used: 97343 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