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_RS03245 BWI76_RS03245 maltodextrin ABC transporter permease
Query= TCDB::Q8DT27 (453 letters) >FitnessBrowser__Koxy:BWI76_RS03245 Length = 427 Score = 319 bits (818), Expect = 1e-91 Identities = 172/426 (40%), Positives = 257/426 (60%), Gaps = 19/426 (4%) Query: 26 SFVIMGFANLMNKQFIKGLLFLLSEIAFLIAFVTQVIPAFSGLLTLGTKTQGMQEKIVDG 85 SF+IMG L++ +IKG +FLL +I +I+ + ++ A GL+TLGT Q + Sbjct: 15 SFLIMGATQLISGHWIKGSVFLLFQIV-VISNINLLLNATQGLITLGTVAQTRSGFDI-- 71 Query: 86 VKLQVAVEGDNSMLMLIFGLASLIFCLVFAYIYWCNLKSARNLYMLKKEGRHIPSFKEDF 145 V GDNS+ ML+ G+ + IF ++YW N+K A+ + SF E Sbjct: 72 ------VAGDNSIFMLVEGVVAFIFLFFSIFVYWLNIKDAQVCEKCHQ------SFTEQL 119 Query: 146 MTLANGRFHMTLMFIPLIGVLLFTILPLVYMICLAFTNYDH-NHLPPKSLFDWVGLANFG 204 T+ + RF ++ I + F I+P++ + ++ TNY +H+PPK+L DWVGL NF Sbjct: 120 RTIYDNRFATIMLAPAFIACIAFIIMPMIITVLVSLTNYSAPHHIPPKNLVDWVGLKNFI 179 Query: 205 NVLNGRM-AGTFFPVLSWTLIWAVFATVTNFLFGVILALIINAKGLKLKKMWRTIFVITI 263 + R+ + TF + WT++WA FAT+ FG +LAL + K + KK WR +F++ Sbjct: 180 TLFELRIWSKTFVGIGVWTVLWAFFATLCTCSFGFLLALALENKKIIAKKAWRVVFILPY 239 Query: 264 AVPQFISLLLMRNFLNDQGPLNAFLEKIGLISHSLPFLSDPTWAKFSIIFVNMWVGIPFT 323 A+P F++LL+ R LN GP+N+ L G+ S+ FLSDP AK ++I V++WVG P+ Sbjct: 240 AIPAFVTLLIFRLLLNGIGPVNSTLNSWGI--DSIGFLSDPLIAKMTVIAVSVWVGAPYF 297 Query: 324 MLVATGIIMNLPSEQIEAAEIDGASKFQIFKSITFPQILLIMMPSLIQQFIGNINNFNVI 383 ML+ TG + N+P + EA+E+DGASKFQ F+ IT P +L + PSL+ F N NNF I Sbjct: 298 MLLITGAMTNIPRDLYEASEVDGASKFQQFREITLPMVLHQVAPSLVMTFAHNFNNFGAI 357 Query: 384 YLLTGGGPTNSQFYQAGSTDLLVTWLYKLTMNAADYNLASVIGIFIFAISAIFSLLAYTH 443 YLLT GGP N ++ AG TD+L+TW+YKLT++ Y +ASVI I IF +IF++ + Sbjct: 358 YLLTEGGPINPEYRFAGHTDILITWIYKLTLDFQQYQIASVISIIIFLFLSIFAIWQFRR 417 Query: 444 TASYKE 449 S+KE Sbjct: 418 MKSFKE 423 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: 575 Number of extensions: 24 Number of successful extensions: 7 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: 453 Length of database: 427 Length adjustment: 32 Effective length of query: 421 Effective length of database: 395 Effective search space: 166295 Effective search space used: 166295 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: 51 (24.3 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