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 RR42_RS12955 RR42_RS12955 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Cup4G11:RR42_RS12955 Length = 367 Score = 337 bits (865), Expect = 2e-97 Identities = 189/384 (49%), Positives = 241/384 (62%), Gaps = 28/384 (7%) Query: 1 MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60 MA ++ + Y G+ K V +D+ I DGEF+V+VGPSGCGKST LRM+AGLE ++GG Sbjct: 1 MAKLSLRNVQKTYAGNVK-VVHGIDMEINDGEFIVIVGPSGCGKSTLLRMVAGLEAISGG 59 Query: 61 AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120 + IGD+ V HL P +RDIAMVFQNYALYPHM+V DNM + LKI G+ K+EI Q+V+ AA Sbjct: 60 EVHIGDKVVNHLEPAERDIAMVFQNYALYPHMSVYDNMAYGLKIRGMDKSEIEQRVKHAA 119 Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180 IL+L L+RKP+ALSGGQRQRVAMGRAIVREP VFL DEPLSNLDAKLRV R ++ Sbjct: 120 GILELAPLLERKPRALSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDAKLRVQMRLELKE 179 Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240 L RRL T++YVTHDQVEAMT+ DR+ VL G ++Q+ +P +Y +PA+ FVA FIGSP Sbjct: 180 LHRRLRTTSMYVTHDQVEAMTLADRMMVLNGGSVEQIGTPLEVYARPASTFVASFIGSPP 239 Query: 241 MNLVEVPITDGG---------VKFGNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVEL 291 MNLV V T+GG K G P L +G+RPEH + Sbjct: 240 MNLVPVTRTNGGQGEAQMRVEQKPGAQGAPATLGHLPMGLHLPERALLGLRPEHIEPCAA 299 Query: 292 GGAVAASLSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEK 351 A+A + V +VE LGAD Y YGT +GG+ +VVR++ Sbjct: 300 HEAIA--------------EIEVRLVEALGADSYAYGT--LGGQ--PVVVRLDSNMPVSS 341 Query: 352 GSTLHVVPRPGETHVFSTSTGERL 375 G L + H F +G+R+ Sbjct: 342 GDRLPITAAAEHLHFFDADSGKRI 365 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: 434 Number of extensions: 21 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: 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