Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate BPHYT_RS05040 BPHYT_RS05040 sugar ABC transporter ATPase
Query= TCDB::P96483 (377 letters) >FitnessBrowser__BFirm:BPHYT_RS05040 Length = 371 Score = 302 bits (773), Expect = 1e-86 Identities = 178/384 (46%), Positives = 241/384 (62%), Gaps = 21/384 (5%) Query: 1 MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60 MA+++ + YP P + ++I IEDG+FL+LVG SGCGKST L M+AGLE V G Sbjct: 1 MASLSIRDVYKTYPNG-VPVLKGVNIDIEDGQFLILVGGSGCGKSTLLNMIAGLETVTKG 59 Query: 61 AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120 I+I + V +L PKDRDIAMVFQ+YALYP MTV +N+ F L I VPK E Q V+ + Sbjct: 60 EIQIDGKTVNNLSPKDRDIAMVFQSYALYPSMTVRENISFGLNIRKVPKNEQTQIVDRVS 119 Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180 L +T LDRKP LSGGQRQRVAMGRA+ R+P +FL DEPLSNLDAKLR+ R++I Sbjct: 120 NTLQITHLLDRKPGQLSGGQRQRVAMGRALARDPVMFLFDEPLSNLDAKLRIEMRSEIKL 179 Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240 L +RLG T VYVTHDQ+EAMT+GDR+AV+KDG++QQ +P+ +YD P+NLFVAGFIG+P Sbjct: 180 LHQRLGTTIVYVTHDQIEAMTLGDRIAVMKDGIVQQFGAPQEIYDSPSNLFVAGFIGAPP 239 Query: 241 MNLVEVPITDGGVKFGNSV-VPVNREALS-------AADKGDRTVTVGVRPEHFDVVELG 292 MN ++ + + G + V R AL+ R V +G+RPE + + Sbjct: 240 MNFIQGKLVEQGAGVALELDTGVARTALNLPFDSAKVRSHVGREVILGLRPER--ITDAR 297 Query: 293 GAVAASLSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKG 352 GA D+A + V V+V+E G D V+ A+V G K +V RV+ P+ Sbjct: 298 GA-----HGDNAKLQP-IEVKVDVIEPTGPDTLVF--AQVNG--KRIVSRVHPASNPQPL 347 Query: 353 STLHVVPRPGETHVFSTSTGERLS 376 + ++ + +F S ER++ Sbjct: 348 ANTTLLFDTSKAVLFDPSNEERIA 371 Lambda K H 0.317 0.135 0.379 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: 400 Number of extensions: 14 Number of successful extensions: 1 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: 377 Length of database: 371 Length adjustment: 30 Effective length of query: 347 Effective length of database: 341 Effective search space: 118327 Effective search space used: 118327 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