Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate BPHYT_RS05040 BPHYT_RS05040 sugar ABC transporter ATPase
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__BFirm:BPHYT_RS05040 Length = 371 Score = 352 bits (903), Expect = e-101 Identities = 183/377 (48%), Positives = 251/377 (66%), Gaps = 15/377 (3%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA + + +YKTYP P +K N+DI+D +F + VG SGCGK+T L MIAGLE +T+G Sbjct: 1 MASLSIRDVYKTYPNGV-PVLKGVNIDIEDGQFLILVGGSGCGKSTLLNMIAGLETVTKG 59 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 + I + VN++ PKDRDIAMVFQ+YALYP MTV +N++FGL +RKVPK E + V + Sbjct: 60 EIQIDGKTVNNLSPKDRDIAMVFQSYALYPSMTVRENISFGLNIRKVPKNEQTQIVDRVS 119 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 L I HLLDRKP LSGGQRQRVA+GRA+ R+P +FL DEPLSNLDAKLR++MR+EI+ Sbjct: 120 NTLQITHLLDRKPGQLSGGQRQRVAMGRALARDPVMFLFDEPLSNLDAKLRIEMRSEIKL 179 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 LHQRL TT++YVTHDQ EAMT+GDRI VM+DG++QQ PQ +Y P N+FVAGFIG+P Sbjct: 180 LHQRLGTTIVYVTHDQIEAMTLGDRIAVMKDGIVQQFGAPQEIYDSPSNLFVAGFIGAPP 239 Query: 241 MNFIRGEIVQDGDAFYFRAPS----ISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDE 296 MNFI+G++V+ G + +L LP + K +G+ V+LG+RPE + D Sbjct: 240 MNFIQGKLVEQGAGVALELDTGVARTALNLP---FDSAKVRSHVGREVILGLRPERITDA 296 Query: 297 EVFMTTYPDSV----LQMQVEVVEHMGSEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLA 352 + D+ ++++V+V+E G + + + IV+RV+P ++ L Sbjct: 297 R---GAHGDNAKLQPIEVKVDVIEPTGPDTLVFAQVNGKRIVSRVHPASNPQPLANTTLL 353 Query: 353 IDLNKIHIFDAETEESI 369 D +K +FD EE I Sbjct: 354 FDTSKAVLFDPSNEERI 370 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: 393 Number of extensions: 15 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: 371 Length adjustment: 30 Effective length of query: 354 Effective length of database: 341 Effective search space: 120714 Effective search space used: 120714 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