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::Q70HW1 (384 letters) >FitnessBrowser__BFirm:BPHYT_RS22760 Length = 384 Score = 324 bits (831), Expect = 2e-93 Identities = 190/385 (49%), Positives = 247/385 (64%), Gaps = 23/385 (5%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA + L + K Y G+ P ++D +L+I + EF VF+GPSGCGK+T LRMIAGLED+T+G Sbjct: 1 MASISLRGVQKAY-GEGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDG 59 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 +L IG + +NDVP R +AMVFQ+YAL+PHM+V++NMAFGLKL K PK E+DR+V+EAA Sbjct: 60 DLSIGGKLMNDVPAAQRGVAMVFQSYALFPHMSVFENMAFGLKLAKTPKDEVDRKVREAA 119 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 +IL + LL+RKPKALSGGQRQRVA+GRAIVREP VFL DEPLSNLDA LR Q R EI + Sbjct: 120 RILQLEALLERKPKALSGGQRQRVAIGRAIVREPGVFLFDEPLSNLDATLRGQTRIEIAR 179 Query: 181 LHQRL-QTTVIYVTHDQTEAMTMGDRIVVM-------RDGVIQQADTPQVVYSQPKNMFV 232 LH++ + +V+YVTHDQ EAMT+ D+IV++ R G I Q P +Y +PK+ FV Sbjct: 180 LHKQFAKASVVYVTHDQIEAMTLADKIVLLHAGKDTERYGSIAQIGAPLELYHRPKSRFV 239 Query: 233 AGFIGSPAMNFIRGEIVQ---DGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVR 289 AGFIGSP MNF+ G + G ++R+P G L+ S A V LGVR Sbjct: 240 AGFIGSPRMNFLPGRVASLDAQGVTITLDHTQETVRVPVNGAG-LQTSQA----VTLGVR 294 Query: 290 PEDLHDEEVFMTTYPDSVLQMQVEVVEHMGSEVYLH-TSIGPNTIVARVNPRHVYHVGSS 348 PE L + D+VL V +VE +G Y+H G +VA+ G Sbjct: 295 PEHLEFVDPSSVAPDDAVLTRTVSLVEQLGEHSYVHLDQPGGAALVAKAPGNTRLAPGER 354 Query: 349 VKLAIDLNKIHIFDAETEESIGFAA 373 L + H+F TE+ GFAA Sbjct: 355 ASLRVPRAACHLF---TED--GFAA 374 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: 425 Number of extensions: 16 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: 384 Length of database: 384 Length adjustment: 30 Effective length of query: 354 Effective length of database: 354 Effective search space: 125316 Effective search space used: 125316 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