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 PfGW456L13_3039 Various polyols ABC transporter, ATP-binding component
Query= TCDB::P96483 (377 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3039 Length = 367 Score = 305 bits (781), Expect = 1e-87 Identities = 169/355 (47%), Positives = 222/355 (62%), Gaps = 35/355 (9%) Query: 24 LDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDIAMVF 83 +D+ + D EF+V VGPSGCGKST LR++AGLE+V+GG I + RD+T + P RD+AMVF Sbjct: 22 IDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTIELDGRDITEVSPAKRDLAMVF 81 Query: 84 QNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGGQRQR 143 Q YALYPHM+V NM FAL +AGV KAE+ +KV EAA+IL+L L+RKPK LSGGQRQR Sbjct: 82 QTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARILELGPMLERKPKQLSGGQRQR 141 Query: 144 VAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEAMTMG 203 VA+GRAIVR P++FL DEPLSNLDA LRV R ++ L + L T +YVTHDQVEAMTM Sbjct: 142 VAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLHKELQATMIYVTHDQVEAMTMA 201 Query: 204 DRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPIT-----------DGG 252 D+V VL G ++QV SP ++Y +PANLFVAGF+G+P M ++ IT D G Sbjct: 202 DKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMGFLKGKITRVDSQGCEVQLDAG 261 Query: 253 VKFGNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAV 312 + +P+ LS VT+G+RPEH ++ + G L V Sbjct: 262 TRVS---LPLGGRHLSVGS----AVTLGIRPEHLELAKPG--------------DCALQV 300 Query: 313 SVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPRPGETHVF 367 + +V E LG+D + + G + L +RV G G TL + H+F Sbjct: 301 TADVSERLGSDTFCHVRTASG---EALTMRVRGDLASRYGETLSLHLDAQHCHLF 352 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: 407 Number of extensions: 21 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: 377 Length of database: 367 Length adjustment: 30 Effective length of query: 347 Effective length of database: 337 Effective search space: 116939 Effective search space used: 116939 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: 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