Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_048058439.1 MMARC5_RS02070 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU3 (247 letters) >NCBI__GCF_000016125.1:WP_048058439.1 Length = 253 Score = 99.8 bits (247), Expect = 5e-26 Identities = 75/240 (31%), Positives = 124/240 (51%), Gaps = 18/240 (7%) Query: 11 LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70 ++ V+GVE Y + L V V KGE+VS++G NGAGKSTL+ I + G++ Sbjct: 2 IVSVDGVEFKYKSTEILKDVKFEVKKGEVVSILGINGAGKSTLIKCINKILPPKKGTITI 61 Query: 71 EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLK--------HFAED 122 E D+ +M ++A+ ++ P+ R MTV + L +G ++K E+ Sbjct: 62 ENLDVNKMDRLDLAK-KVGYVPQ-RSNGNYMTVFDALLLGR-KPHIKWEISQKDIEITEN 118 Query: 123 VEKIFTLFPRLKERHAQRG-GTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKG 181 V K+ L +++A R LSGGE Q + IGR L+ PKL+LLDEP+ L Sbjct: 119 VLKLLDL-----DKYALRNTNELSGGELQKVIIGRVLVQEPKLILLDEPTNNLDLKNQLE 173 Query: 182 IFEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAY 241 + ++ ++ +E +T +V + ALR S + ++ +GK+ G GKE++ + Y Sbjct: 174 VMRILKDVSVSENITSIIVMHDINLALRYSDKFLMLKDGKIFAEG-GKEIINTQNIVEVY 232 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: 161 Number of extensions: 9 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: 247 Length of database: 253 Length adjustment: 24 Effective length of query: 223 Effective length of database: 229 Effective search space: 51067 Effective search space used: 51067 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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