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 AZOBR_RS08670 AZOBR_RS08670 arginine ABC transporter ATP-binding protein
Query= uniprot:A0A1N7U8S3 (276 letters) >FitnessBrowser__azobra:AZOBR_RS08670 Length = 258 Score = 228 bits (580), Expect = 1e-64 Identities = 129/276 (46%), Positives = 176/276 (63%), Gaps = 21/276 (7%) Query: 1 MNQSAQALAAYPVDEPVAQPVTAAIKLQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGA 60 M Q+A A + EP+ +Q +G+HK YGE VLK + L+ +G+ I + G Sbjct: 1 MAQTAGAARTFAQGEPI---------IQCQGVHKWYGEFHVLKNIDLSVAKGERIVICGP 51 Query: 61 SGSGKSTMLRCINFLEQPDAGVITLDGISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQH 120 SGSGKSTM+RC+N LE+ G I +DGI + + ++ +R + MVFQH Sbjct: 52 SGSGKSTMIRCLNRLEEHQKGSIVVDGIEL----------TGNLKNIELVRREVGMVFQH 101 Query: 121 FNLWSHMTVLENITMAPRRVLDVSAAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQR 180 FNL+ H+TVLEN T+AP V AEAE+ A YL +V + + A +YP LSGGQQQR Sbjct: 102 FNLFPHLTVLENCTLAPIWVRKKPKAEAEEMAMRYLKRVRIAEQ-AHKYPGQLSGGQQQR 160 Query: 181 VAIARALAMEPEIILFDEPTSALDPELVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSS 240 VAIAR+L M P+++LFDEPTSALDPE+V EVL V+ LAE+G TML VTHEMGFA+ V+ Sbjct: 161 VAIARSLCMSPKVMLFDEPTSALDPEMVKEVLDVMIGLAEDGMTMLCVTHEMGFAKSVAD 220 Query: 241 QVLFLHQGR-VEEHGDARILDQPNSERLQQFLSNRL 275 +V+F+ +G VE++ + P S+R + FLS L Sbjct: 221 RVIFMDRGEIVEQNTPNEFFNHPQSDRTKLFLSQIL 256 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: 8 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: 276 Length of database: 258 Length adjustment: 25 Effective length of query: 251 Effective length of database: 233 Effective search space: 58483 Effective search space used: 58483 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