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 WP_008510542.1 BIBO1_RS17490 ABC transporter ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >NCBI__GCF_000182725.1:WP_008510542.1 Length = 333 Score = 296 bits (759), Expect = 4e-85 Identities = 172/370 (46%), Positives = 232/370 (62%), Gaps = 45/370 (12%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M +L+L +++KRY +++ NL+++D EFI+FVGPSGCGKST LR IAGLED++ G Sbjct: 1 MGSLQLKSVHKRY--GAQEVLKDINLEVNDGEFIIFVGPSGCGKSTLLRSIAGLEDVSAG 58 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 + I+ + + P R IAMVFQ+YALYPH++V NM GLK KD+I RV +A+ Sbjct: 59 QVLINGEDVTVTPPSRRGIAMVFQSYALYPHLTVKANMGLGLKQAGAPKDEIEGRVAKAS 118 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 +L L +L R+PA+LSGGQRQRVA+GRA+VR+ ++FL DEPLSNLDA LRV R EIAK Sbjct: 119 AMLALEPYLARRPAELSGGQRQRVAIGRALVRNPELFLFDEPLSNLDAALRVQTRLEIAK 178 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 +HR + AT IYVTHDQ EAMTLADRIV+++A GRIEQIG+P ELYN P N Sbjct: 179 LHRELKATMIYVTHDQVEAMTLADRIVVLNA----------GRIEQIGSPMELYNRPDNL 228 Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDI 300 FVAGFIGSP MNF E G G + T+GIRPE + Sbjct: 229 FVAGFIGSPQMNFIEAA-------------------------RIGATGAR-TIGIRPEHL 262 Query: 301 SSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEF-TARVNARDSHSPGEKVQLT 359 S + + + ++ +E LG++++LYV+ + TAR+ ++ + + LT Sbjct: 263 SVSR------ESGTWKGKVIHAEHLGADTILYVETETAGLVTARLFGEQHYNEDDVIFLT 316 Query: 360 FNIAKGHFFD 369 K H+FD Sbjct: 317 PEEGKTHYFD 326 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: 346 Number of extensions: 16 Number of successful extensions: 2 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: 333 Length adjustment: 29 Effective length of query: 348 Effective length of database: 304 Effective search space: 105792 Effective search space used: 105792 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 24 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