Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate BPHYT_RS35680 BPHYT_RS35680 sugar ABC transporter ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__BFirm:BPHYT_RS35680 Length = 360 Score = 345 bits (885), Expect = 1e-99 Identities = 193/368 (52%), Positives = 244/368 (66%), Gaps = 16/368 (4%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA V L I+K Y G T+ V +LDI D EF V VGPSGCGK+T +RM+AGLE+I+ G Sbjct: 1 MAAVQLSGIFKRY-GDTQ-VVHGIDLDIDDGEFVVLVGPSGCGKSTLMRMVAGLEEISGG 58 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 +L IG R N + P+ R+I+MVFQ+YALYPH++VY+N+AFG ++RK A R++ AA Sbjct: 59 DLMIGGTRANSLAPQQRNISMVFQSYALYPHLSVYENIAFGPRIRKESSASFKPRIEAAA 118 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 K+L++ LDR P+ALSGGQRQRVA+GRA+VREP +FL DEPLSNLDAKLRVQMR EI+ Sbjct: 119 KMLNLGGYLDRLPRALSGGQRQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQMRTEIKA 178 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 LHQRL+ TVIYVTHDQ EAMTM DRIVVM G I+Q P +Y P N+FVA F+GSP+ Sbjct: 179 LHQRLKNTVIYVTHDQIEAMTMADRIVVMNAGRIEQIGRPLELYDHPANLFVASFLGSPS 238 Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLK---ASGAIGKPVVLGVRPEDLHDEE 297 MNF G I A + ++L L G VL+ AS +G V LGVRPE + Sbjct: 239 MNFAEGVI-----ASRAQGQGLALNLTGGGEIVLEGAPASAVVGAKVTLGVRPEHIET-- 291 Query: 298 VFMTTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDLNK 357 MT PD+ M+VEVVE G+E +L+ IG +T R G V L + Sbjct: 292 --MTPTPDAT--MEVEVVEPTGAETHLYGKIGGSTWCVTTRQRSKIEPGQRVTLRLPAEH 347 Query: 358 IHIFDAET 365 IH+FD E+ Sbjct: 348 IHLFDTES 355 Lambda K H 0.321 0.138 0.395 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: 404 Number of extensions: 13 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: 384 Length of database: 360 Length adjustment: 30 Effective length of query: 354 Effective length of database: 330 Effective search space: 116820 Effective search space used: 116820 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: 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