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 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::P96483 (377 letters) >FitnessBrowser__ANA3:7026050 Length = 376 Score = 200 bits (508), Expect = 6e-56 Identities = 101/225 (44%), Positives = 152/225 (67%), Gaps = 8/225 (3%) Query: 20 AVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDI 79 A+ L++ I++GE + L+GPSG GK+T LR++AGLE + G I G+RDVT + +DR + Sbjct: 17 ALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIHFGNRDVTQVHVRDRRV 76 Query: 80 AMVFQNYALYPHMTVADNMGFALKIAGVPK------AEIRQKVEEAAKILDLTQYLDRKP 133 VFQNYAL+ HMTVADN+ F L++ +PK AEI+++V +++ L R P Sbjct: 77 GFVFQNYALFRHMTVADNVAFGLEV--IPKKQRPSKAEIQKRVSHLLEMVQLGHLAQRYP 134 Query: 134 KALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVT 193 + LSGGQ+QR+A+ RA+ +P+V L+DEP LDAK+R R + SL L T+V+VT Sbjct: 135 EQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLRSLHDELKFTSVFVT 194 Query: 194 HDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGS 238 HDQ EA+ + DRV V+ +G ++QV++P +Y +P + FV F+G+ Sbjct: 195 HDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFLGN 239 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: 347 Number of extensions: 17 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: 376 Length adjustment: 30 Effective length of query: 347 Effective length of database: 346 Effective search space: 120062 Effective search space used: 120062 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