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_593 Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-)
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_593 Length = 386 Score = 310 bits (795), Expect = 3e-89 Identities = 173/384 (45%), Positives = 247/384 (64%), Gaps = 27/384 (7%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M TL+L N+ K Y +++N L I+D EF++ VGPSGCGKST + IAGLE+I+ G Sbjct: 1 MATLELRNVNKTYGAGLPDTLKNIELKINDGEFLILVGPSGCGKSTLMNCIAGLENISGG 60 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 + +DD ++ SPKDRDIAMVFQ+YALYP MSV +N+AFGLK+RK +I++ V A Sbjct: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVA 120 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 ++L + L RKP LSGGQ+QRVAMGRA+ R K++L DEPLSNLDAKLRV MR E+ Sbjct: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 +H+R+ TT+YVTHDQ EAMTL D++ +M G I+Q GTP+++YN PAN Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKD----------GIIQQFGTPKDIYNNPANL 230 Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLA-LPQGQEKI-----LEEKGYLGKKVTLG 294 FVA FIGSP MNF + RL +DG +A L GQ + +++ G ++V LG Sbjct: 231 FVASFIGSPPMNFIPL-----RLQRKDGRLVALLDSGQARCELPLGMQDAGLEDREVILG 285 Query: 295 IRPEDISSDQIVHETFPNA--SVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSP 352 +RPE I ++ + PN ++ A++ V+E G +++++V T+ R+ + + Sbjct: 286 MRPEQI----VLAGSEPNGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAV 341 Query: 353 GEKVQLTFNIAKGHFFDLETEKRI 376 GE + L F+ +K FD +T +R+ Sbjct: 342 GETLTLQFDPSKVLLFDAKTGERL 365 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: 424 Number of extensions: 16 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: 386 Length adjustment: 30 Effective length of query: 347 Effective length of database: 356 Effective search space: 123532 Effective search space used: 123532 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