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 PP_1018 PP_1018 mannose/glucose ABC transporter - ATP binding subunit
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Putida:PP_1018 Length = 384 Score = 310 bits (795), Expect = 3e-89 Identities = 176/383 (45%), Positives = 241/383 (62%), Gaps = 23/383 (6%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M TL+L N+ K Y + ++++ L I D EF++ VGPSGCGKST + IAGLE IT G Sbjct: 1 MATLELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGG 60 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 + ID++ ++ SPKDRDIAMVFQ+YALYP MSV EN+ FGLK+RK + I++ V A Sbjct: 61 AILIDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVA 120 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 ++L + L RKPA LSGGQ+QRVAMGRA+ R K++L DEPLSNLDAKLRV MR E+ Sbjct: 121 KLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 +H+R+ TT+YVTHDQ EAMTL D++ +M G I+Q GTPQ++YN+PAN+ Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKD----------GIIQQFGTPQQIYNDPANQ 230 Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLA-LPQGQEKILEEKGYL-----GKKVTLG 294 FVA FIGSP MNF V RL QDG LA L GQ + G G+++ LG Sbjct: 231 FVASFIGSPPMNFIPV-----RLARQDGRLLALLDSGQARCELPLGEAADALEGREIILG 285 Query: 295 IRPEDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSPGE 354 IRPE I+ P ++ A++ V+E G + +++V T+ R+ + G+ Sbjct: 286 IRPEQIALGAADGNGLP--AIRAEVQVTEPTGPDLLVFVTLNQTKVCCRLAPDVACRVGD 343 Query: 355 KVQLTFNIAKGHFFDLETEKRIN 377 + L F+ A+ FD +R++ Sbjct: 344 TLNLQFDPARVLLFDAANGERLH 366 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: 379 Number of extensions: 18 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: 384 Length adjustment: 30 Effective length of query: 347 Effective length of database: 354 Effective search space: 122838 Effective search space used: 122838 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