Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate BPHYT_RS13580 BPHYT_RS13580 arginine ABC transporter ATP-binding protein
Query= uniprot:A0A1N7U8S3 (276 letters) >FitnessBrowser__BFirm:BPHYT_RS13580 Length = 248 Score = 252 bits (643), Expect = 6e-72 Identities = 135/246 (54%), Positives = 176/246 (71%), Gaps = 12/246 (4%) Query: 27 LQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVITLD 86 ++V+ IHKR+ + VLKGVSLN +G V+ LIG SGSGKST+LRCIN LE+ DAG IT++ Sbjct: 2 IKVDSIHKRFHDQHVLKGVSLNVERGQVVCLIGPSGSGKSTLLRCINGLERHDAGEITVE 61 Query: 87 GISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLDVSAA 146 G +++ + Q+ LR ++ MVFQ FNL+ H T LEN+ P V + A Sbjct: 62 GRTVDAKS----------KQIHELRAQVGMVFQRFNLFPHRTALENVFEGPVFVKKQARA 111 Query: 147 EAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALDPE 206 +A +RAR LDKVGL R+ + +PA LSGGQQQRVAIARALAMEP+ ILFDEPTSALDPE Sbjct: 112 QARERARHLLDKVGLAHRM-NAHPAELSGGQQQRVAIARALAMEPKAILFDEPTSALDPE 170 Query: 207 LVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHGD-ARILDQPNSE 265 LVGEVL V++ LA++G TM++VTHEM FAR+V+ +V FLH G + E G A + D+P Sbjct: 171 LVGEVLGVMRQLADDGMTMIVVTHEMAFAREVADRVCFLHDGAIHEEGSAAELFDRPRHA 230 Query: 266 RLQQFL 271 R ++FL Sbjct: 231 RTREFL 236 Lambda K H 0.319 0.133 0.372 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: 210 Number of extensions: 12 Number of successful extensions: 4 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: 276 Length of database: 248 Length adjustment: 25 Effective length of query: 251 Effective length of database: 223 Effective search space: 55973 Effective search space used: 55973 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: 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