Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_048058439.1 MMARC5_RS02070 ABC transporter ATP-binding protein
Query= uniprot:G8ALJ1 (236 letters) >NCBI__GCF_000016125.1:WP_048058439.1 Length = 253 Score = 97.1 bits (240), Expect = 3e-25 Identities = 70/235 (29%), Positives = 120/235 (51%), Gaps = 8/235 (3%) Query: 1 MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60 ++ V GV Y + E LK V E+ GE+VS++G NGAGKSTL+ I + G IT Sbjct: 2 IVSVDGVEFKYKSTEILKDVKFEVKKGEVVSILGINGAGKSTLIKCINKILPPKKGTITI 61 Query: 61 EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITAKPGSFANE----LERV 116 E D+ +M +L + + P+ R M+V + L +G + + E V Sbjct: 62 ENLDVNKMDRLDLAK-KVGYVPQ-RSNGNYMTVFDALLLGRKPHIKWEISQKDIEITENV 119 Query: 117 LTLFPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAV 176 L L L + + +SGGE Q + IGR L+ +P+L+LLDEP+ L ++ + + Sbjct: 120 LKLLD-LDKYALRNTNELSGGELQKVIIGRVLVQEPKLILLDEPTNNLDLKNQLEVMRIL 178 Query: 177 KDINREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAY 231 KD++ + +T +V + AL+ + + ++ +GK+ G G E++ + + Y Sbjct: 179 KDVSVSENITSIIVMHDINLALRYSDKFLMLKDGKIFAEG-GKEIINTQNIVEVY 232 Lambda K H 0.320 0.136 0.377 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: 151 Number of extensions: 10 Number of successful extensions: 2 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: 236 Length of database: 253 Length adjustment: 24 Effective length of query: 212 Effective length of database: 229 Effective search space: 48548 Effective search space used: 48548 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