Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate SMc04140 SMc04140 ABC transporter ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__Smeli:SMc04140 Length = 360 Score = 333 bits (853), Expect = 6e-96 Identities = 189/350 (54%), Positives = 241/350 (68%), Gaps = 5/350 (1%) Query: 6 LTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDGT 65 L VEK YG + V+ I+L I GE VFVGPSGCGKSTLLRMIAGLE+I+GGTL +D Sbjct: 7 LQKVEKRYGALDVIHGIDLTIDPGEFAVFVGPSGCGKSTLLRMIAGLEEISGGTLMLDSD 66 Query: 66 VVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQ 125 +N+V PA+RGIAMVFQSYALYPHM+V +N++F L+ A +AEI+ V AAE LQ+ + Sbjct: 67 RMNEVAPARRGIAMVFQSYALYPHMSVYKNLAFGLETAGFKKAEIEPKVRRAAEILQIEK 126 Query: 126 YLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPE 185 LDR PKALSGGQRQRVAIGR+IVR+P+++LFDEPLSNLDA LRV R+EI++L + Sbjct: 127 LLDRKPKALSGGQRQRVAIGRAIVREPRIFLFDEPLSNLDAELRVQMRVEISRLHRDL-G 185 Query: 186 STMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLLPG 245 +TM+YVTHDQVEAMT+A +IVVL G I QVG+PL+LY P N FVA FIGSPKMN L Sbjct: 186 NTMIYVTHDQVEAMTMADKIVVLNSGRIEQVGAPLDLYNNPVNRFVAGFIGSPKMNFLKA 245 Query: 246 KIIG-TGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGGDYVFEGKVA 304 +I TG++T +E+ GG + + G V G+RPE + A GG + V Sbjct: 246 RIADVTGSETAIEVC-GGTIRLPRRLNGATQGQDVTFGIRPEHL-SAREGGIELATVNVE 303 Query: 305 ITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVF 354 I E LG T+LY P + T+ L+G K +G + +P++ HVF Sbjct: 304 IVENLGGETMLYGITPDRQQLTVA-LEGQQKVERGSNLAVHFDPSRCHVF 352 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: 392 Number of extensions: 16 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: 373 Length of database: 360 Length adjustment: 30 Effective length of query: 343 Effective length of database: 330 Effective search space: 113190 Effective search space used: 113190 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: 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