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 Ac3H11_2941 Various polyols ABC transporter, ATP-binding component
Query= TCDB::P96483 (377 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2941 Length = 350 Score = 316 bits (809), Expect = 7e-91 Identities = 177/351 (50%), Positives = 227/351 (64%), Gaps = 27/351 (7%) Query: 20 AVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDI 79 A+ +D+ I+ GEF+V VGPSGCGKST LR++AGLE ++GG++ + RD+T P RD+ Sbjct: 18 AIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSLMLDGRDITDQPSSKRDL 77 Query: 80 AMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGG 139 AMVFQ+YALYPHM+V +NM FALK+A V K I +KV+ AA+IL+LTQYL R PK LSGG Sbjct: 78 AMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARILNLTQYLQRTPKELSGG 137 Query: 140 QRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEA 199 QRQRVA+GRAIVR P+VFL DEPLSNLDA LR TR +IA L R LG TT+YVTHDQVEA Sbjct: 138 QRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLHRDLGATTIYVTHDQVEA 197 Query: 200 MTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVKFGNSV 259 MT+ DRV VL+DG+++QV +P +YDKPAN FVA FIG+P MN+V V Sbjct: 198 MTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQMNVVPV---------DKLP 248 Query: 260 VPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAVSVNVVEE 319 PV ++A AA G +G+RPE+ V G P G V+++E Sbjct: 249 QPVQQQA-PAAPAGAAVGAIGLRPENITVRTTGA------------TPVG--GQVDLIEA 293 Query: 320 LGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPRPGETHVFSTS 370 LGA+ +Y T G + V R N R G + + + H F T+ Sbjct: 294 LGAETLIYVTTPGGAQ---FVSRQNDRTDLRVGDAVSLDIDASQAHWFDTA 341 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: 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: 350 Length adjustment: 29 Effective length of query: 348 Effective length of database: 321 Effective search space: 111708 Effective search space used: 111708 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