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 GFF4321 PS417_22130 sugar ABC transporter ATPase
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__WCS417:GFF4321 Length = 386 Score = 308 bits (789), Expect = 2e-88 Identities = 176/382 (46%), Positives = 238/382 (62%), Gaps = 23/382 (6%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M TL+L N+ K Y +++N L I + EF++ VGPSGCGKST + IAGLE IT G Sbjct: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 + I D+ ++ SPKDRDIAMVFQ+YALYP MSV EN+ FGLK+RK + DI+ V A Sbjct: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 ++L + L RKP LSGGQ+QRVAMGRA+ R K++L DEPLSNLDAKLRV MR E+ Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 +H+R+ TT+YVTHDQ EAMTL D++ +M G I+Q GTP+E+YN PAN+ Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKD----------GIIQQFGTPKEIYNNPANQ 230 Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLA-LPQGQEKI-----LEEKGYLGKKVTLG 294 FVA FIGSP MNF + RL +DG +A L GQ + E G + V LG Sbjct: 231 FVASFIGSPPMNFVPL-----RLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILG 285 Query: 295 IRPEDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSPGE 354 +RPE I E +S+ A++ V+E G +++++V+ T+ R+ + GE Sbjct: 286 LRPEQIM--LAAGEGDSASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGE 343 Query: 355 KVQLTFNIAKGHFFDLETEKRI 376 + L F+ +K FD T +R+ Sbjct: 344 TLTLQFDPSKVLLFDANTGERL 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: 376 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: 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