Align glucose transporter, periplasmic substrate-binding component (characterized)
to candidate Pf6N2E2_1455 Xylose ABC transporter, periplasmic xylose-binding protein XylF
Query= reanno::Phaeo:GFF3639 (341 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1455 Length = 333 Score = 226 bits (575), Expect = 8e-64 Identities = 130/320 (40%), Positives = 187/320 (58%), Gaps = 6/320 (1%) Query: 9 ALAFAATASMAFAEDVTVGVSWSNFQEERWKTDEAAIKAALEAKGATYVSADAQSSSAKQ 68 ALA + MA A +G S + + ERW D AA E A A ++ KQ Sbjct: 12 ALALLSLPVMADAAHPKIGFSIDDLRLERWSRDRDYFVAAAEKLDAKVFVQSADANEQKQ 71 Query: 69 LSDIESLIAQGVDALIVLAQDAQAIGPAVQAAADEGIPVVAYDRLIEDGRA-FYLTFDNV 127 +S IE+LI++GVD ++++ +A + AV A GI VV+YDRLI + Y++FDN Sbjct: 72 ISQIENLISRGVDVIVIVPFNATVLTNAVAEAKKAGIKVVSYDRLILNADIDAYISFDNE 131 Query: 128 EVGRMQARAVLEAQPSGNYVMIKGSPTDPNADFLRGGQQEIIQAAIDSGDIKIVGEAYTD 187 +VG MQA VL+A P GNY ++ G+PTD NA LR GQ +++Q AID GDIKIVG+ + Sbjct: 132 KVGEMQASGVLKAAPKGNYFLLGGAPTDNNAKVLREGQMKVLQPAIDKGDIKIVGQQWVK 191 Query: 188 GWLPANAQRNMEQILTANDNKVDAVVASNDGTAGGVVAALTAQGMEG-IAVSGQDGDHAA 246 W P A +E LT N+NK+D +VASND TAGG + AL AQ M G + +SGQD D AA Sbjct: 192 EWNPTEALSIVENALTRNNNKIDGIVASNDATAGGAIQALAAQKMAGKVPISGQDADLAA 251 Query: 247 LNRVAKGTQTVSVWKDARDLGKAAANIAVEMAEGAVMGDVAGGAAWTSPAGTELTARFLE 306 + RV GTQT++V+K + + AA ++V++A + ++ ++ L Sbjct: 252 VKRVIDGTQTMTVYKPLKLIASEAAKLSVQLAR----NEKPTFSSQYDNGSKKVDTILLT 307 Query: 307 PIPVTADNLSVVVDAGWITK 326 P P+T DN+ ++ G+ TK Sbjct: 308 PTPLTKDNIDLLEKDGFYTK 327 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: 209 Number of extensions: 7 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: 341 Length of database: 333 Length adjustment: 28 Effective length of query: 313 Effective length of database: 305 Effective search space: 95465 Effective search space used: 95465 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