Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate Pf6N2E2_1649 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1649 Length = 384 Score = 335 bits (860), Expect = 9e-97 Identities = 184/362 (50%), Positives = 240/362 (66%), Gaps = 8/362 (2%) Query: 4 LLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFID 63 L L ++ K G ++ + L+I GEFVVFVGPSGCGKSTLLR+IAGL+ I GD+ ID Sbjct: 4 LKLDNVNKQLGGARILRDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICDGDLLID 63 Query: 64 GERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQL 123 G RVND+ P +RG+ MVFQSYALYPHM+VYDN++FG+++A+ K + RV A +LQL Sbjct: 64 GRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKASLRERVLKTAQILQL 123 Query: 124 TPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERM 183 L R P+ LSGGQRQRVA+GRA+ R P + LFDEPLSNLDA+LRV R EIA+L R+ Sbjct: 124 DKLLQRKPRELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHGRL 183 Query: 184 SDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVI 243 +TMIYVTHDQVEAMTLAD+IVVL+ G IEQVG+P ELYE PA+ FVA F+GSP MN + Sbjct: 184 G-STMIYVTHDQVEAMTLADKIVVLNGGRIEQVGSPRELYEHPASRFVAGFLGSPKMNFL 242 Query: 244 PATITATGQQTAVS--LAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFEGT 301 PA + + G+ + + L G + D A G + G+RPE + + A G Sbjct: 243 PARLHSPGETSQIDSPLLGMTPLPFDSAHLAV--GSPLTLGIRPEHMSLKAAQGSAGVGV 300 Query: 302 VSI--VEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDTNGQS 359 V + VE LG T +++E E+EP+I + A GD+V +HLFD +G + Sbjct: 301 VGVVGVEYLGSETYVHLES-GEDEPLICRCEVNAGWRVGDRVELQLAFGSVHLFDADGTA 359 Query: 360 YR 361 R Sbjct: 360 LR 361 Lambda K H 0.320 0.137 0.387 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: 382 Number of extensions: 18 Number of successful extensions: 5 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: 362 Length of database: 384 Length adjustment: 30 Effective length of query: 332 Effective length of database: 354 Effective search space: 117528 Effective search space used: 117528 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: 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