Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate WP_091519694.1 BM253_RS04260 phosphate ABC transporter ATP-binding protein
Query= TCDB::O30494 (367 letters) >NCBI__GCF_900115115.1:WP_091519694.1 Length = 248 Score = 117 bits (293), Expect = 3e-31 Identities = 73/242 (30%), Positives = 131/242 (54%), Gaps = 14/242 (5%) Query: 4 LKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVS-----EG 58 L +NL F ++K I + + E +GPSGCGKSTLLR + ++ G Sbjct: 5 LSAENLNISFGEKHVLKNISVSFAEHEITALIGPSGCGKSTLLRSFNRMHDLFPDAKING 64 Query: 59 TIELDGRDITE----VTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGV--DKQLVES 112 ++ L+ D+ + VT ++ + MVFQ +P S+ +N+++ L + + +K++V+ Sbjct: 65 SLHLEELDLYDRHVPVTEIRKRIGMVFQKANPFPK-SIYENIAYGLKINNLPCNKEVVQK 123 Query: 113 KVNEAARILELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQM 172 + EA E+ L+ +LSGGQ+QR+ I RA+ P++ L DEP S LD + Sbjct: 124 ALEEAYLWDEVKNDLKMPATRLSGGQQQRLCIARAVALRPEVILMDEPCSALDPV--STL 181 Query: 173 RLELARLHKELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAG 232 ++E H + + T++ VTH+ +A +ADK V + G +++ G+ E+++ P N A Sbjct: 182 KIEELIKHLKKKYTIVIVTHNMQQAQRIADKTVFMYLGEVKEEGTTDEIFNHPKNEMTAN 241 Query: 233 FL 234 ++ Sbjct: 242 YI 243 Lambda K H 0.319 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: 181 Number of extensions: 11 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: 367 Length of database: 248 Length adjustment: 27 Effective length of query: 340 Effective length of database: 221 Effective search space: 75140 Effective search space used: 75140 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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