Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate BPHYT_RS22760 BPHYT_RS22760 sugar ABC transporter ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__BFirm:BPHYT_RS22760 Length = 384 Score = 285 bits (728), Expect = 2e-81 Identities = 172/382 (45%), Positives = 230/382 (60%), Gaps = 28/382 (7%) Query: 1 MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60 MA+++ + +Y G P ++ +LEI + EF V +GPSGCGKST LRM+AGLE++TDG Sbjct: 1 MASISLRGVQKAY-GEGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDG 59 Query: 61 AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120 + IG K + V R +AMVFQ+YAL+PHM+V ENM F LK+A +DE++++V EAA Sbjct: 60 DLSIGGKLMNDVPAAQRGVAMVFQSYALFPHMSVFENMAFGLKLAKTPKDEVDRKVREAA 119 Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180 L L LERKPKALSGGQRQRVA+GRAIVR P VFL DEPLSNLDA LR QTR +IA Sbjct: 120 RILQLEALLERKPKALSGGQRQRVAIGRAIVREPGVFLFDEPLSNLDATLRGQTRIEIAR 179 Query: 181 LQRKLG-VTTVYVTHDQTEALTMGDRIAVL---KD----GYLQQVGAPRELYDRPANVFV 232 L ++ + VYVTHDQ EA+T+ D+I +L KD G + Q+GAP ELY RP + FV Sbjct: 180 LHKQFAKASVVYVTHDQIEAMTLADKIVLLHAGKDTERYGSIAQIGAPLELYHRPKSRFV 239 Query: 233 AGFIGSPAMNLGTFSVKDGDATSGHARIKLSPETLAAMTP----EDNGRITIGFRPEALE 288 AGFIGSP MN V DA + + ET+ + + +T+G RPE LE Sbjct: 240 AGFIGSPRMNFLPGRVASLDAQGVTITLDHTQETVRVPVNGAGLQTSQAVTLGVRPEHLE 299 Query: 289 II-PEGESTDLSIPIK-LDFVEELGSDSFLYGKLVGEGDLGSSSEDVPESGQIVVRAAPN 346 + P + D ++ + + VE+LG S+++ D P +V +A N Sbjct: 300 FVDPSSVAPDDAVLTRTVSLVEQLGEHSYVH-------------LDQPGGAALVAKAPGN 346 Query: 347 AAPAPGSVFHARIVEGGQHNFS 368 APG R+ H F+ Sbjct: 347 TRLAPGERASLRVPRAACHLFT 368 Lambda K H 0.316 0.135 0.380 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: 407 Number of extensions: 15 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: 376 Length of database: 384 Length adjustment: 30 Effective length of query: 346 Effective length of database: 354 Effective search space: 122484 Effective search space used: 122484 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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