Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate Pf1N1B4_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115 Length = 381 Score = 285 bits (728), Expect = 2e-81 Identities = 159/353 (45%), Positives = 218/353 (61%), Gaps = 7/353 (1%) Query: 4 LEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIG 63 L++ N+ K+ G + L+ + + + +GEF+V +G SGCGKSTLL +IAGL GGD+LI Sbjct: 4 LKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLID 63 Query: 64 ERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLLQI 123 R V + P++R + MVFQSYALYP++SV NI FGL++ + + + V TA++LQ+ Sbjct: 64 GRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQL 123 Query: 124 ENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQML 183 + LL RKP +LSGGQRQRVA+GRA+ R P + LFDEPLSNLDA LR++MR E+ RLH L Sbjct: 124 DKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRL 183 Query: 184 RTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMNILD 243 +T++YVTHDQ+EAMTLA +I V+ GR+EQ+ +P E+Y+RPA+ +VAGF+GSP MN L Sbjct: 184 GSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLS 243 Query: 244 AEMTANG---LKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTASV 300 A + G L + LP + A AG + +GIRPE + L A + V Sbjct: 244 ARLQTPGETSLVDTLVWGITSLPFDSSNLA-AGTPLSLGIRPEHVSLKAADGTAGVV--V 300 Query: 301 EVVELTGPELVTTATVGSQRITACLPPRTAVGM-GSAHAFTFDGTALHLFDPE 352 VE G E G C +A G D LHLFD + Sbjct: 301 TAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDAD 353 Lambda K H 0.320 0.136 0.385 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: 369 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: 360 Length of database: 381 Length adjustment: 30 Effective length of query: 330 Effective length of database: 351 Effective search space: 115830 Effective search space used: 115830 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