Align ABC transporter for L-Arginine, putative ATPase component (characterized)
to candidate BPHYT_RS13580 BPHYT_RS13580 arginine ABC transporter ATP-binding protein
Query= reanno::BFirm:BPHYT_RS07685 (263 letters) >FitnessBrowser__BFirm:BPHYT_RS13580 Length = 248 Score = 263 bits (672), Expect = 3e-75 Identities = 139/247 (56%), Positives = 171/247 (69%), Gaps = 12/247 (4%) Query: 12 LAVQDIHKRYGDNEVLKGVSLNANKGDVISIIGASGSGKSTFLRCINFLERPNAGQIVVD 71 + V IHKR+ D VLKGVSLN +G V+ +IG SGSGKST LRCIN LER +AG+I V+ Sbjct: 2 IKVDSIHKRFHDQHVLKGVSLNVERGQVVCLIGPSGSGKSTLLRCINGLERHDAGEITVE 61 Query: 72 GEMVKTKTDRAGNLEVADHKQLQRIRTKLAMVFQHFNLWAHMNVLENIVEAPIHVLGLKR 131 G V K+ KQ+ +R ++ MVFQ FNL+ H LEN+ E P+ V R Sbjct: 62 GRTVDAKS-----------KQIHELRAQVGMVFQRFNLFPHRTALENVFEGPVFVKKQAR 110 Query: 132 KEAEDRAREYLEKVGLAPRLEKQYPSHLSGGQQQRVAIARALAMNPDVMLFDEPTSALDP 191 +A +RAR L+KVGLA R+ +P+ LSGGQQQRVAIARALAM P +LFDEPTSALDP Sbjct: 111 AQARERARHLLDKVGLAHRMNA-HPAELSGGQQQRVAIARALAMEPKAILFDEPTSALDP 169 Query: 192 ELVGEVLKVMQKLAEEGRTMIVVTHEMGFARNVSNHVMFLHQGRTEEEGLPAEVLSAPRS 251 ELVGEVL VM++LA++G TMIVVTHEM FAR V++ V FLH G EEG AE+ PR Sbjct: 170 ELVGEVLGVMRQLADDGMTMIVVTHEMAFAREVADRVCFLHDGAIHEEGSAAELFDRPRH 229 Query: 252 ERLKQFL 258 R ++FL Sbjct: 230 ARTREFL 236 Lambda K H 0.318 0.133 0.374 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: 216 Number of extensions: 13 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: 263 Length of database: 248 Length adjustment: 24 Effective length of query: 239 Effective length of database: 224 Effective search space: 53536 Effective search space used: 53536 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