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 GFF3011 HP15_2955 ATP-binding component of ABC transporter
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Marino:GFF3011 Length = 372 Score = 325 bits (834), Expect = 1e-93 Identities = 182/384 (47%), Positives = 251/384 (65%), Gaps = 23/384 (5%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M+ L+L +I K YP +++ ++DI EF++ VGPSGCGKST + IAGLE IT+G Sbjct: 1 MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 ++ +D K ++ PKDRDIAMVFQ+YALYP MSV EN+AFGLK+R K +I++ V A Sbjct: 61 SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 ++L ++ + +KPA+LSGGQ+QRVAMGRA+ R +++L DEPLSNLDAKLRV MR EI K Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 +H+R+ T +YVTHDQ EAMTLADRI ++ G ++Q+GTP+E+Y+ P N Sbjct: 181 LHQRLKTTIVYVTHDQIEAMTLADRIAVLKD----------GELQQLGTPKEVYDRPENL 230 Query: 241 FVAGFIGSPAMNFFEVTVE------KERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLG 294 FVAGF+GSPAM+F VTVE + + DG S+ LP + L ++ +GKKV LG Sbjct: 231 FVAGFMGSPAMSFVPVTVEQGEGGLQAEVRGNDGRSVKLP--VPEFLADR--VGKKVILG 286 Query: 295 IRPEDIS--SDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSP 352 IRPE I+ DQ +T A I V+E G + + ++ T R++ + Sbjct: 287 IRPEHITQPQDQKNDQTLV-AKGEFTIEVTEPTGPDVIALIQLNDTNVHCRIDPEHPVTW 345 Query: 353 GEKVQLTFNIAKGHFFDLETEKRI 376 GE +L F++ K FFD ETEKRI Sbjct: 346 GETAELMFDMKKVVFFDPETEKRI 369 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: 389 Number of extensions: 22 Number of successful extensions: 4 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: 372 Length adjustment: 30 Effective length of query: 347 Effective length of database: 342 Effective search space: 118674 Effective search space used: 118674 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