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 HSERO_RS18940 HSERO_RS18940 sn-glycerol-3-phosphate ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >FitnessBrowser__HerbieS:HSERO_RS18940 Length = 364 Score = 301 bits (772), Expect = 1e-86 Identities = 183/383 (47%), Positives = 237/383 (61%), Gaps = 28/383 (7%) Query: 1 MATVTFDKATRIYPGSDKPAVDQL---DIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDV 57 MA + + + Y G+ AVD + D I DGEF+V+VGPSGCGKST LRM+AGLE++ Sbjct: 1 MAAIHLKQVRKTY-GAGTKAVDVIHGIDAEIADGEFIVMVGPSGCGKSTLLRMVAGLEEI 59 Query: 58 NGGAIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVE 117 + G I IGDR V L PK+RDIAMVFQNYALYPHMTV NM + LKI G+ K+EI +V+ Sbjct: 60 SSGQIVIGDRVVNDLEPKERDIAMVFQNYALYPHMTVYQNMAYGLKIQGLSKSEIDARVQ 119 Query: 118 EAAKILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQ 177 AA IL+L L+R P+ LSGGQRQRVAMGRAIVR+P VFL DEPLSNLDAKLRV R + Sbjct: 120 RAAAILELGALLERTPRQLSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLE 179 Query: 178 IASLQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIG 237 I L L T++YVTHDQVEAMT+G R+ V+ G+ +Q+ +P +Y +PA FVA FIG Sbjct: 180 IQKLHASLRTTSLYVTHDQVEAMTLGQRMIVMNRGVAEQIGTPAEVYARPATTFVASFIG 239 Query: 238 SPAMNLVEVPITDGGVKF----GN-SVVPVNREALSAADKGDRTVTVGVRPEHFDVVELG 292 SP MNL++ ++ G F GN S + + L+ A +R +GVRPEH + G Sbjct: 240 SPPMNLLQGKLSADGASFEVSKGNASDILRLPQPLTGAAGQER--ILGVRPEHLLPILDG 297 Query: 293 GAVAASLSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKG 352 A A L++ V +VE LGA+ V+ A GG+ LV+R G Sbjct: 298 SA-------------AQLSLEVELVEALGAELLVH--ARCGGQA--LVLRCPANVQVRTG 340 Query: 353 STLHVVPRPGETHVFSTSTGERL 375 + G+ H F + R+ Sbjct: 341 QRIGASFGAGDVHWFDVKSTRRI 363 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: 377 Number of extensions: 13 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: 364 Length adjustment: 30 Effective length of query: 347 Effective length of database: 334 Effective search space: 115898 Effective search space used: 115898 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