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 BWI76_RS23390 BWI76_RS23390 oligogalacturonide ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Koxy:BWI76_RS23390 Length = 375 Score = 310 bits (793), Expect = 5e-89 Identities = 180/388 (46%), Positives = 241/388 (62%), Gaps = 26/388 (6%) Query: 1 MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60 MA V F+K ++Y K AV +D+ I DGEF+V+VGPSGC KST+LRMLAGLE ++GG Sbjct: 1 MAEVIFNKLEKVYSNGFK-AVHGIDLKIADGEFMVIVGPSGCAKSTTLRMLAGLETISGG 59 Query: 61 AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120 +RIG++ V +L PK R IAMVFQNYALYPHMTV +N+ F LK++ +PK +I +V EAA Sbjct: 60 EVRIGEKIVNNLAPKARGIAMVFQNYALYPHMTVRENLAFGLKLSKLPKDQIEAQVNEAA 119 Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180 KIL+L + LDR P+ LSGGQ QRVA+GRAIV++P VFL DEPLSNLDAKLR S R +I+ Sbjct: 120 KILELEELLDRLPRQLSGGQAQRVAVGRAIVKKPDVFLFDEPLSNLDAKLRASMRIRISD 179 Query: 181 LQRRL-----GITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGF 235 L ++L TTVYVTHDQ EAMTMGDR+ V+K G + QVD+P N+Y KP N+FVAGF Sbjct: 180 LHKQLKKSGKPATTVYVTHDQTEAMTMGDRICVMKLGHIMQVDTPDNLYHKPKNMFVAGF 239 Query: 236 IGSPAMNLVEVPITDGG----VKFGNSVVPVNREALSAAD-KGDRTVTVGVRPEHFDVVE 290 IG+P MN+ + + + G+ ++P+N S D ++ V GVRPE + Sbjct: 240 IGAPEMNIRPSQLVEQAGRLHLTVGDGLLPLNDRLQSKVDTHKNQQVFFGVRPEFVSI-- 297 Query: 291 LGGAVAASLSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPE 350 D A + VE +G + +VY E+ V + + E Sbjct: 298 ----------SDEPFAEGSCTGEMVRVENMGHEFFVY-LKVADYELTARVPSDEAKPMIE 346 Query: 351 KG--STLHVVPRPGETHVFSTSTGERLS 376 KG +H + H+F T + +S Sbjct: 347 KGLHRKVHFKFDLNKCHIFDAKTEQNIS 374 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: 393 Number of extensions: 12 Number of successful extensions: 3 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: 375 Length adjustment: 30 Effective length of query: 347 Effective length of database: 345 Effective search space: 119715 Effective search space used: 119715 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