Align MalF, 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 BWI76_RS01825 BWI76_RS01825 maltose ABC transporter permease MalF
Query= TCDB::Q8DT27 (453 letters) >FitnessBrowser__Koxy:BWI76_RS01825 Length = 514 Score = 147 bits (371), Expect = 8e-40 Identities = 82/248 (33%), Positives = 135/248 (54%), Gaps = 8/248 (3%) Query: 198 VGLANFGNVLNGR-MAGTFFPVLSWTLIWAVFATVTNFLFGVILALIINAKGLKLKKMWR 256 +G NF V + FF + WT++++V + G++LA ++ + LK K ++R Sbjct: 259 IGWDNFTRVFQDEGIQKPFFAIFVWTVVFSVLTVILTVAVGMVLACLVQWEALKGKAIYR 318 Query: 257 TIFVITIAVPQFISLLLMRNFLNDQ-GPLNAFLEKIGLISHSLPFLSDPTWAKFSIIFVN 315 + ++ AVP FIS+L+ + N G +N L + I + + SDPT A+ II VN Sbjct: 319 VLLILPYAVPSFISILIFKGLFNQSFGEINMMLSALFGIKPA--WFSDPTTARTMIIIVN 376 Query: 316 MWVGIPFTMLVATGIIMNLPSEQIEAAEIDGASKFQIFKSITFPQILLIMMPSLIQQFIG 375 W+G P+ M++ G++ +P + EA+ +DGA+ FQ F IT P ++ + P +I F Sbjct: 377 TWLGYPYMMILCMGLLKAIPDDLYEASAMDGATPFQNFFKITLPLLIKPLTPLMIASFAF 436 Query: 376 NINNFNVIYLLTGGGPTN-SQFYQAGSTDLLVTWLYKLTMNAA---DYNLASVIGIFIFA 431 N NNF +I LLT GGP AG TDLLV++ Y++ D+ LA+ I IF Sbjct: 437 NFNNFVLIQLLTNGGPDRLGTTTPAGYTDLLVSYTYRIAFEGGGGQDFGLAAAIATLIFL 496 Query: 432 ISAIFSLL 439 + + +++ Sbjct: 497 LVGLLAIV 504 Score = 28.9 bits (63), Expect = 4e-04 Identities = 12/23 (52%), Positives = 16/23 (69%) Query: 162 LIGVLLFTILPLVYMICLAFTNY 184 L G+ LF + PL+ I +AFTNY Sbjct: 72 LAGMGLFVLFPLICTIAIAFTNY 94 Lambda K H 0.329 0.143 0.431 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: 549 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 453 Length of database: 514 Length adjustment: 34 Effective length of query: 419 Effective length of database: 480 Effective search space: 201120 Effective search space used: 201120 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 52 (24.6 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