Align ABC transporter for Lactose, ATPase component (characterized)
to candidate Pf6N2E2_1649 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1649 Length = 384 Score = 352 bits (904), Expect = e-102 Identities = 187/360 (51%), Positives = 248/360 (68%), Gaps = 6/360 (1%) Query: 3 ELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTI 62 +L+L +V K GG +++ V L+I +GEFVVFVGPSGCGKSTLLR+IAGL+ I GDL I Sbjct: 3 KLKLDNVNKQLGGARILRDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICDGDLLI 62 Query: 63 DDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILE 122 D R+ND++P +RG+ MVFQSYALYPHM+V +N+ F L+ A +A + +RV + A IL+ Sbjct: 63 DGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKASLRERVLKTAQILQ 122 Query: 123 LGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQ 182 L LL RKP++LSGGQRQRVA+GRA+ R P I LFDEPLSNLDA LRV MR EIARLH + Sbjct: 123 LDKLLQRKPRELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHGR 182 Query: 183 LATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNFL 242 L +T++YVTHDQVEAMTLADKIVV+ G +EQVGSP +LY+ PA+ FVAGF+GSPKMNFL Sbjct: 183 LGSTMIYVTHDQVEAMTLADKIVVLNGGRIEQVGSPRELYEHPASRFVAGFLGSPKMNFL 242 Query: 243 KGVIEIDEDQAYARLPDYGDAKIPV-TLQAAAGTAVTIGIRPEHFD---EAGPAALD-LA 297 + + + P G +P + A G+ +T+GIRPEH G A + + Sbjct: 243 PARLHSPGETSQIDSPLLGMTPLPFDSAHLAVGSPLTLGIRPEHMSLKAAQGSAGVGVVG 302 Query: 298 IDMLEHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVFDGEGKRLR 357 + +E+LG ET+ + G E ++ + G + GDR+ + SV +FD +G LR Sbjct: 303 VVGVEYLGSETYVHL-ESGEDEPLICRCEVNAGWRVGDRVELQLAFGSVHLFDADGTALR 361 Lambda K H 0.321 0.139 0.396 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: 435 Number of extensions: 15 Number of successful extensions: 3 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: 358 Length of database: 384 Length adjustment: 30 Effective length of query: 328 Effective length of database: 354 Effective search space: 116112 Effective search space used: 116112 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 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