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 PfGW456L13_1210 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1210 Length = 374 Score = 229 bits (584), Expect = 9e-65 Identities = 132/307 (42%), Positives = 183/307 (59%), Gaps = 26/307 (8%) Query: 9 IYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLYIDDKL 68 + K Y + ++ V++ NLDI EF+ +GPSG GK+T+L M+AG E T G + + + Sbjct: 20 VQKSY-DGENLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEILLAGRA 78 Query: 69 MNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEILGLTEF 128 +N+ P RDI MVFQNYAL+PHM+V EN+AF L +R K D++ RV ++ L F Sbjct: 79 INNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRGMNKSDVSARVKRVLSMVQLDAF 138 Query: 129 LERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHRRIGAT 188 +R PA LSGGQ+QRVA+ RA+V + ++ LMDEPL LD +LR M+ EI +H+R+G T Sbjct: 139 AQRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHLHQRLGVT 198 Query: 189 TIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVAGFIGS 248 +YVTHDQ EA+T++DR+ + G I+QI P+ LY EP N FVA FIG Sbjct: 199 VVYVTHDQGEALTMSDRVAVFHQ----------GEIQQIAPPRTLYEEPKNTFVANFIG- 247 Query: 249 PAMNFFEVTVEKERLVNQDG----LSLALPQGQEKILEEKGYLGKKVTLGIRPEDI---- 300 E RL +Q G + L + E + G G+ VTL IRPE + Sbjct: 248 ------ENNRLNGRLHSQTGDRCIVELGRGEKVEALAVNVGQTGEPVTLSIRPERVSLNG 301 Query: 301 SSDQIVH 307 SSDQ V+ Sbjct: 302 SSDQCVN 308 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: 304 Number of extensions: 14 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: 374 Length adjustment: 30 Effective length of query: 347 Effective length of database: 344 Effective search space: 119368 Effective search space used: 119368 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