Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate Pf1N1B4_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115 Length = 381 Score = 333 bits (853), Expect = 6e-96 Identities = 179/351 (50%), Positives = 225/351 (64%), Gaps = 25/351 (7%) Query: 20 LQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQID 79 L+L + K G +L+ + L++ GEFV+FVGPSGCGKSTLLR IAGL+ G + ID Sbjct: 4 LKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLID 63 Query: 80 GVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGMLSL 139 G V + P +RG+ MVFQSYALYPH++V DN+ GLK A K + E+V K A +L L Sbjct: 64 GRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQL 123 Query: 140 EPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLHRSL 199 + L R+P ELSGGQRQRVA+GRA+ REP + LFDEPLSNLDA+LRV R EIARLH L Sbjct: 124 DKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRL 183 Query: 200 KATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMNFIE 259 +TMIYVTHDQVEAMTLADKIVVLN GR+EQVGSP ELY RPA+ FVAGF+GSP+MNF+ Sbjct: 184 GSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLS 243 Query: 260 A-------------------------AKLGDGEAKTIGIRPEHIGLSRESGDWKGKVIHV 294 A + L G ++GIRPEH+ L G V V Sbjct: 244 ARLQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKAADGTAGVVVTAV 303 Query: 295 EHLGADTIIYIESETVGLLTVRLFGEHRYATDDIVHATPVIGSMHRFDADG 345 E+LG++T +++E+ L R + D V + ++H FDADG Sbjct: 304 EYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDADG 354 Lambda K H 0.320 0.137 0.393 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: 396 Number of extensions: 13 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: 352 Length of database: 381 Length adjustment: 30 Effective length of query: 322 Effective length of database: 351 Effective search space: 113022 Effective search space used: 113022 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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