Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate BPHYT_RS05040 BPHYT_RS05040 sugar ABC transporter ATPase
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__BFirm:BPHYT_RS05040 Length = 371 Score = 303 bits (775), Expect = 7e-87 Identities = 172/361 (47%), Positives = 235/361 (65%), Gaps = 25/361 (6%) Query: 1 MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60 MA+++ +D +YP P +K N++I DG+FL+LVG SGCGKST L M+AGLE VT G Sbjct: 1 MASLSIRDVYKTYPNGV-PVLKGVNIDIEDGQFLILVGGSGCGKSTLLNMIAGLETVTKG 59 Query: 61 AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120 I I K V +++P+DRDIAMVFQ+YALYP MTV EN+ F L I ++E + VD + Sbjct: 60 EIQIDGKTVNNLSPKDRDIAMVFQSYALYPSMTVRENISFGLNIRKVPKNEQTQIVDRVS 119 Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180 TL +T L+RKP LSGGQRQRVAMGRA+ R+P +FL DEPLSNLDAKLR++ R++I Sbjct: 120 NTLQITHLLDRKPGQLSGGQRQRVAMGRALARDPVMFLFDEPLSNLDAKLRIEMRSEIKL 179 Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240 L ++LG T VYVTHDQ EA+T+GDRIAV+KDG +QQ GAP+E+YD P+N+FVAGFIG+P Sbjct: 180 LHQRLGTTIVYVTHDQIEAMTLGDRIAVMKDGIVQQFGAPQEIYDSPSNLFVAGFIGAPP 239 Query: 241 MN-LGTFSVKDG-----DATSGHARIKLSPETLAAMTPEDNGR-ITIGFRPEALEII--P 291 MN + V+ G + +G AR L+ +A GR + +G RPE + Sbjct: 240 MNFIQGKLVEQGAGVALELDTGVARTALNLPFDSAKVRSHVGREVILGLRPERITDARGA 299 Query: 292 EGESTDLS-IPIKLDFVEELGSDSFLYGKLVGEGDLGSSSEDVPESGQIVVRAAPNAAPA 350 G++ L I +K+D +E G D+ ++ ++ G+ +IV R P + P Sbjct: 300 HGDNAKLQPIEVKVDVIEPTGPDTLVFAQVNGK--------------RIVSRVHPASNPQ 345 Query: 351 P 351 P Sbjct: 346 P 346 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: 369 Number of extensions: 11 Number of successful extensions: 2 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: 371 Length adjustment: 30 Effective length of query: 346 Effective length of database: 341 Effective search space: 117986 Effective search space used: 117986 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