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 209027 DVU0098 polyamine ABC transporter, ATP-binding protein
Query= TCDB::P96483 (377 letters) >MicrobesOnline__882:209027 Length = 368 Score = 236 bits (602), Expect = 8e-67 Identities = 129/310 (41%), Positives = 191/310 (61%), Gaps = 22/310 (7%) Query: 17 DKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKD 76 D A+D +D+ I +GEFL L+GPSGCGK+T LR+++G E + G I + + + PP+ Sbjct: 19 DTCALDNIDLEIRNGEFLTLLGPSGCGKTTILRLISGFEKPDAGVITLKGQRMDDAPPEA 78 Query: 77 RDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKAL 136 R + VFQNYAL+PHM+V +N+GF L++ PK EI ++V +A +++ L + DR+P+ L Sbjct: 79 RQVNTVFQNYALFPHMSVRENVGFGLRMQRRPKDEIARRVHDALRMVHLEAHADRRPRQL 138 Query: 137 SGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQ 196 SGGQ+QRVA+ RA+V P V L+DEP S LD KLR + +I LQR+LGIT V+VTHDQ Sbjct: 139 SGGQQQRVAIARAVVNNPLVLLLDEPFSALDYKLRKQMQLEIKHLQRQLGITFVFVTHDQ 198 Query: 197 VEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVKFG 256 EA M DRV V+ DG ++Q+ SP+ +Y++PANL+VA F+G +N++ I G Sbjct: 199 EEAFAMSDRVVVMNDGKIEQIGSPQEIYEEPANLYVARFVGE--INILNAVI---AANHG 253 Query: 257 NSVVPVNREALSAADKGDRT------VTVGVRPEHFDVVELGGAVAASLSKDSADAPAGL 310 + + E ++ + RT V V +RPE V L + D PAG Sbjct: 254 DGLYDAVIEGVTFPIRSQRTFAPGDKVNVLLRPEDLRVYTL-----------TEDRPAGP 302 Query: 311 AVSVNVVEEL 320 ++ + E + Sbjct: 303 HLTGRIEESV 312 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: 382 Number of extensions: 13 Number of successful extensions: 1 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: 368 Length adjustment: 30 Effective length of query: 347 Effective length of database: 338 Effective search space: 117286 Effective search space used: 117286 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