Align glucose transporter, periplasmic substrate-binding component (characterized)
to candidate SM_b20902 SM_b20902 sugar uptake ABC transporter substrate-binding protein precursor
Query= reanno::Phaeo:GFF3639 (341 letters) >FitnessBrowser__Smeli:SM_b20902 Length = 345 Score = 437 bits (1123), Expect = e-127 Identities = 225/342 (65%), Positives = 268/342 (78%), Gaps = 4/342 (1%) Query: 1 MKFLSGVSALAFAATASMAFAEDVTVGVSWSNFQEERWKTDEAAIKAALEAKGATYVSAD 60 +K ++G + +A + S A A+D+ +GVSWSNFQEERWKTDEAAIKAALEA G Y+SAD Sbjct: 5 LKLMAGAAIIA--SMHSAAIAKDLVIGVSWSNFQEERWKTDEAAIKAALEASGDKYISAD 62 Query: 61 AQSSSAKQLSDIESLIAQGVDALIVLAQDAQAIGPAVQAAADEGIPVVAYDRLIEDGRAF 120 AQSS+AKQL+DIESLIAQG +ALIVLAQD+ AIGPA++ AA EGIPVV YDRLIE+ AF Sbjct: 63 AQSSAAKQLTDIESLIAQGANALIVLAQDSDAIGPAIEKAAAEGIPVVGYDRLIENPDAF 122 Query: 121 YLTFDNVEVGRMQARAVLEAQPSGNYVMIKGSPTDPNADFLRGGQQEIIQAAIDSGDIKI 180 Y+TFDN EVGR+QAR V + +P GN+V IKGS DPNADFL GQ E+++ AID+G IK Sbjct: 123 YITFDNKEVGRLQAREVFKQKPEGNFVFIKGSSADPNADFLFSGQLEVLKEAIDAGKIKN 182 Query: 181 VGEAYTDGWLPANAQRNMEQILTANDNKVDAVVASNDGTAGGVVAALTAQGMEG-IAVSG 239 VGEAYTDGW P NAQ+NMEQ LTANDNKVDAVVASNDGTAGG +AAL AQG+ G + VSG Sbjct: 183 VGEAYTDGWKPENAQKNMEQFLTANDNKVDAVVASNDGTAGGAIAALDAQGLAGSVPVSG 242 Query: 240 QDGDHAALNRVAKGTQTVSVWKDARDLGKAAANIAVEMAEGAVMGDVAGGAAWT-SPAGT 298 QD D AALNRVA GTQTVSVWKD+R+LGK AA IAV +A G M +V G + P G Sbjct: 243 QDADKAALNRVALGTQTVSVWKDSRELGKKAAEIAVALAGGKTMDEVEGVQTFNGGPKGV 302 Query: 299 ELTARFLEPIPVTADNLSVVVDAGWITKEALCQGVTNGPAPC 340 + + FL P+ +T DNL+VV+DAGWI+KE CQG + A C Sbjct: 303 AMKSVFLAPLAITKDNLNVVIDAGWISKEEACQGAKSDVAAC 344 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: 356 Number of extensions: 15 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: 345 Length adjustment: 29 Effective length of query: 312 Effective length of database: 316 Effective search space: 98592 Effective search space used: 98592 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 Apr 09 2024. 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