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 AO356_05180 AO356_05180 sugar ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_05180 Length = 386 Score = 300 bits (768), Expect = 4e-86 Identities = 171/385 (44%), Positives = 236/385 (61%), Gaps = 30/385 (7%) Query: 1 MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60 MAT+ + Y + ++++I+DGEFL+LVGPSGCGKST + +AGLE + GG Sbjct: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKDGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 Query: 61 AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120 AI IGD+DV+ + PKDRDIAMVFQ+YALYP M+V +N+ F LKI + ++ I ++V A Sbjct: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMNQSAIDEEVNRVA 120 Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180 K+L + L+RKP LSGGQ+QRVAMGRA+ R P+++L DEPLSNLDAKLRV RT++ Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240 + +RL TTVYVTHDQ+EAMT+GD+VAV+KDG++QQ +P+++Y PANLFVA FIGSP Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYTNPANLFVASFIGSPP 240 Query: 241 MNLVE----------VPITDGGVKFGNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVE 290 MN + + + D G +P+ + A DR V +G+RPE + Sbjct: 241 MNFIPLRLQRKDGRLLALLDSGQ--ARCELPM---GMQDAGLEDREVILGMRPEQ---IM 292 Query: 291 LGGAVAASLSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPE 350 L G+ L A+ V V E G D V+ V + R+ P+ Sbjct: 293 LAGSEPNGLPTIRAE--------VQVTEPTGPDTLVF----VSLNDTKVCCRLAPDVAPQ 340 Query: 351 KGSTLHVVPRPGETHVFSTSTGERL 375 G TL + P + +F +GERL Sbjct: 341 VGETLTLQFDPSKVLLFDAQSGERL 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: 429 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: 386 Length adjustment: 30 Effective length of query: 347 Effective length of database: 356 Effective search space: 123532 Effective search space used: 123532 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