Align L-Arginine ABC transporter, ATPase component (characterized)
to candidate Dsui_1462 Dsui_1462 ABC-type antimicrobial peptide transport system, ATPase component
Query= reanno::pseudo5_N2C3_1:AO356_18715 (254 letters) >FitnessBrowser__PS:Dsui_1462 Length = 267 Score = 141 bits (356), Expect = 1e-38 Identities = 89/210 (42%), Positives = 133/210 (63%), Gaps = 14/210 (6%) Query: 18 VLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNNEELKLVAGKDGAM 77 VL+ +S AAG+ ++++G SGSGKST L I +++P +G + VAG+D A Sbjct: 59 VLERISFNIAAGEFLALMGPSGSGKSTLLNLIAGIDRPDSGTLS--------VAGQDIA- 109 Query: 78 KAADPKQLQRMRSR-LSMVFQHFNLWSHMTALENIMEAPVHVLGVAKAEAREKAEHYLNK 136 A + +L R+ + +FQ +NL +TALEN+ E P+ + + KAE RE+AE L+ Sbjct: 110 -ALEEAELAAWRAENVGFIFQFYNLMPVLTALENV-ELPLLLKNLGKAERRERAELALSM 167 Query: 137 VGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPELVGDVLKVMQALA 196 VG+A R D P +SGG+QQRVAIARAL +P +++ DEPT LD E GD+L ++Q L Sbjct: 168 VGLADRMDHTPNELSGGQQQRVAIARALITDPTLIVADEPTGDLDRESAGDILHLLQRLN 227 Query: 197 VE-GRTMVVVTHEMGFAREVSNQLVFLHKG 225 E G+T+V+VTH+ A E ++ ++ L KG Sbjct: 228 DELGKTIVMVTHDQR-AAESAHAIMHLEKG 256 Lambda K H 0.317 0.132 0.369 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: 162 Number of extensions: 6 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: 254 Length of database: 267 Length adjustment: 24 Effective length of query: 230 Effective length of database: 243 Effective search space: 55890 Effective search space used: 55890 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 (21.7 bits) S2: 47 (22.7 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