Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate Pf6N2E2_1649 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1649 Length = 384 Score = 311 bits (798), Expect = 1e-89 Identities = 182/360 (50%), Positives = 234/360 (65%), Gaps = 6/360 (1%) Query: 4 LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63 LKL V K G ++L +++L+I GE +VFVGPSGCGKSTLLR+IAGL+ I G L ID Sbjct: 4 LKLDNVNKQLGGARILRDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICDGDLLID 63 Query: 64 GTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQL 123 G VND+ P +RG+ MVFQSYALYPHM+V +N+SF LK+AK +A + V A+ LQL Sbjct: 64 GRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKASLRERVLKTAQILQL 123 Query: 124 GQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAM 183 + L R P+ LSGGQRQRVA+GR++ R+P + LFDEPLSNLDA+LRV R EIA+L + Sbjct: 124 DKLLQRKPRELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHGRL 183 Query: 184 PESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLL 243 STM+YVTHDQVEAMTLA +IVVL GG I QVGSP ELYE P + FVA F+GSPKMN L Sbjct: 184 -GSTMIYVTHDQVEAMTLADKIVVLNGGRIEQVGSPRELYEHPASRFVAGFLGSPKMNFL 242 Query: 244 PGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDM-VEAAPGGDYVFEGK 302 P ++ G + ++ G + S +G+ + +G+RPE M ++AA G V Sbjct: 243 PARLHSPGETSQIDSPLLGMTPLPFDSAHLAVGSPLTLGIRPEHMSLKAAQGSAGVGVVG 302 Query: 303 VAITEALGEVTLLYFEAPSGED-PTIGKLQGIHKDLKGQVTRLTAEPAKVHVF-KDGVSL 360 V E LG T ++ E SGED P I + + G L VH+F DG +L Sbjct: 303 VVGVEYLGSETYVHLE--SGEDEPLICRCEVNAGWRVGDRVELQLAFGSVHLFDADGTAL 360 Lambda K H 0.316 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: 404 Number of extensions: 18 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: 373 Length of database: 384 Length adjustment: 30 Effective length of query: 343 Effective length of database: 354 Effective search space: 121422 Effective search space used: 121422 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 (21.6 bits) S2: 50 (23.9 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