Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate BPHYT_RS22760 BPHYT_RS22760 sugar ABC transporter ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__BFirm:BPHYT_RS22760 Length = 384 Score = 327 bits (838), Expect = 4e-94 Identities = 186/369 (50%), Positives = 241/369 (65%), Gaps = 16/369 (4%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 MA I + + K Y G PV+ +DL IG+ EF V LGPSGCGKST+LRMIAGLED++ G Sbjct: 1 MASISLRGVQKAYGEGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDGD 60 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 L IGG ++ND+PA +R VAMVFQ+YAL+PHMSV++N+AFGL+ K P E+DR+VRE A Sbjct: 61 LSIGGKLMNDVPAAQRGVAMVFQSYALFPHMSVFENMAFGLKLAKTPKDEVDRKVREAAR 120 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 +L LEALLERKP+A+SGGQ+QR AI RAI++ P VFLFDEPLSNLDA LR Q R +I RL Sbjct: 121 ILQLEALLERKPKALSGGQRQRVAIGRAIVREPGVFLFDEPLSNLDATLRGQTRIEIARL 180 Query: 181 HQRL-RTTTVYVTHDQLEAMTLADRVILMQDGR-------IVQAGSPAELYRYPRNLFAA 232 H++ + + VYVTHDQ+EAMTLAD+++L+ G+ I Q G+P ELY P++ F A Sbjct: 181 HKQFAKASVVYVTHDQIEAMTLADKIVLLHAGKDTERYGSIAQIGAPLELYHRPKSRFVA 240 Query: 233 GFIGTPAMNFLSGTVQRQDGQ-LFIETAH-QRWALTGERFSRLRHAMAVKLAVRPDHVRI 290 GFIG+P MNFL G V D Q + I H Q + L+ + AV L VRP+H+ Sbjct: 241 GFIGSPRMNFLPGRVASLDAQGVTITLDHTQETVRVPVNGAGLQTSQAVTLGVRPEHLEF 300 Query: 291 AGEREPA---ASLTCPVSVELVEILGADALL-TTRCGDQTLTALVPADRLPQPGATLTLA 346 A A LT VS LVE LG + + + G L A P + PG +L Sbjct: 301 VDPSSVAPDDAVLTRTVS--LVEQLGEHSYVHLDQPGGAALVAKAPGNTRLAPGERASLR 358 Query: 347 LDQHELHVF 355 + + H+F Sbjct: 359 VPRAACHLF 367 Lambda K H 0.321 0.137 0.403 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: 385 Number of extensions: 14 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: 406 Length of database: 384 Length adjustment: 31 Effective length of query: 375 Effective length of database: 353 Effective search space: 132375 Effective search space used: 132375 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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