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 Pf1N1B4_4847 Various polyols ABC transporter, ATP-binding component
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4847 Length = 367 Score = 310 bits (793), Expect = 5e-89 Identities = 179/375 (47%), Positives = 238/375 (63%), Gaps = 24/375 (6%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M LK+ N+ K + ++ +L+++DKEF+VFVGPSGCGKST LR+IAGLE+++ G Sbjct: 1 MANLKIKNLQKGFEGFS--IIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGG 58 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 + +D + + + SP RD+AMVFQ YALYPHMSV +NM+F L L K ++ K+V EAA Sbjct: 59 TIELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVGEAA 118 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 IL L LERKP LSGGQRQRVA+GRAIVR+ K+FL DEPLSNLDA LRV MR E+ + Sbjct: 119 RILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLR 178 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 +H+ + AT IYVTHDQ EAMT+AD++V+++ G+IEQ+G+P +LY++PAN Sbjct: 179 LHKELQATMIYVTHDQVEAMTMADKVVVLNG----------GKIEQVGSPLDLYHQPANL 228 Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKG---YLGKKVTLGIRP 297 FVAGF+G+P M F + V + VN + L G L G +G VTLGIRP Sbjct: 229 FVAGFLGTPKMGFLKGKVTR---VNGQSCEVLLDAGTRITLPLSGANLSVGGAVTLGIRP 285 Query: 298 EDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTE-FTARVNARDSHSPGEKV 356 E + Q T VTAD VSE LGS++ +V S E T RV + GE + Sbjct: 286 EHLELAQPGDCTL---QVTAD--VSERLGSDTFCHVLTSSGEALTMRVRGDLASRYGETL 340 Query: 357 QLTFNIAKGHFFDLE 371 L + H FD + Sbjct: 341 SLHLDAEHCHLFDAD 355 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: 343 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: 367 Length adjustment: 30 Effective length of query: 347 Effective length of database: 337 Effective search space: 116939 Effective search space used: 116939 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: 49 (23.5 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