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 GFF2690 PGA1_c27320 putative sugar ABC transporter, ATP-binding protein
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Phaeo:GFF2690 Length = 349 Score = 300 bits (767), Expect = 5e-86 Identities = 171/355 (48%), Positives = 219/355 (61%), Gaps = 26/355 (7%) Query: 21 VDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDIA 80 VD D+ I D EFLVL+GPSGCGK+T++RM+AGLE + G I + V L PKDRD+A Sbjct: 19 VDNFDLTIADKEFLVLLGPSGCGKTTTMRMIAGLESASEGDILVDGNRVNELEPKDRDVA 78 Query: 81 MVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGGQ 140 MVFQ+YALYP+M V +N+ F LK+ GV +KV A+ +++L ++L RKP LSGGQ Sbjct: 79 MVFQSYALYPNMNVYENIRFPLKVRGVDAKTHDEKVRRASAMVELDEFLHRKPAELSGGQ 138 Query: 141 RQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEAM 200 RQRVA+ RAIVREP VFLMDEPLSNLDAKLRVSTR QI +L L +TT+YVTHDQ+EAM Sbjct: 139 RQRVALARAIVREPNVFLMDEPLSNLDAKLRVSTRAQIKNLSHELAVTTIYVTHDQIEAM 198 Query: 201 TMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVKFGNSVV 260 T+ DRV V+ G++QQV SP +YD+PAN FVA FIGSPAMNL+E GG+ G Sbjct: 199 TLADRVVVMNKGVVQQVGSPTEIYDRPANAFVASFIGSPAMNLME-----GGLSGGR--F 251 Query: 261 PVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAVSVNVVEEL 320 ++ D VT+G R E VV+ GG + A + +E L Sbjct: 252 TAQHTDIAGLSGQDGPVTLGFRAEDASVVDSGGQINA---------------PIYTMELL 296 Query: 321 GADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPRPGETHVFSTSTGERL 375 G V T +GG + + R + ++HV H+F T TG RL Sbjct: 297 GDATMV--TVRIGGVLVSVKADKTFRAEIDDMVSIHV--PTDHCHLFDTQTGARL 347 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: 395 Number of extensions: 18 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: 349 Length adjustment: 29 Effective length of query: 348 Effective length of database: 320 Effective search space: 111360 Effective search space used: 111360 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