Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate 202699 SO3602 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__MR1:202699 Length = 376 Score = 196 bits (497), Expect = 1e-54 Identities = 107/269 (39%), Positives = 165/269 (61%), Gaps = 18/269 (6%) Query: 3 TLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNL 62 +++L NI K++ + ++ NLDI + E I +GPSG GK+T LR+IAGLE G++ Sbjct: 2 SIRLTNISKKF--GQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGHI 59 Query: 63 YIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKD----DINKRVHE 118 + ++ + +DR + VFQNYAL+ HM+V +N+AFGL++ K+ +I KRV Sbjct: 60 HFGNRDVTQVHVRDRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSAAEIQKRVSH 119 Query: 119 AAEILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEI 178 E++ L +R P LSGGQ+QR+A+ RA+ +V L+DEP LDAK+R +R + Sbjct: 120 LLEMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWL 179 Query: 179 AKIHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPA 238 +H + T+++VTHDQ EA+ L+DR+V+MS G IEQ+ TP ELY +P Sbjct: 180 RSLHDELKFTSVFVTHDQDEALELSDRVVVMSN----------GNIEQVNTPIELYAQPN 229 Query: 239 NKFVAGFIGSPAMNFFEVTVEKERLVNQD 267 ++FV F+G+ +N FE ++ R N D Sbjct: 230 SRFVFDFLGN--VNRFEANWQQNRWTNGD 256 Lambda K H 0.318 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: 320 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: 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 (21.7 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