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 WP_035586711.1 EK17_RS00965 ABC transporter ATP-binding protein
Query= uniprot:A0A1N7U8S3 (276 letters) >NCBI__GCF_000744435.1:WP_035586711.1 Length = 223 Score = 126 bits (317), Expect = 4e-34 Identities = 81/233 (34%), Positives = 134/233 (57%), Gaps = 22/233 (9%) Query: 27 LQVEGIHKRY--GEH--EVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGV 82 ++ +GI+K + G+ EVLK ++L ++ +++L+G SGSGKST+L + L PD+G Sbjct: 4 IEAKGIYKSFKSGQETIEVLKSINLEIKKSQMVALMGVSGSGKSTLLHILGLLSAPDSGE 63 Query: 83 ITLDGISIEMRQGRAGTRAPHQDQLQNLRTR-LAMVFQHFNLWSHMTVLENITMAPRRVL 141 + G I+ ++ L R + + VFQ ++L +T+LENI M P + Sbjct: 64 VIFSGSKIDFTS---------EENLALFRNKHIGFVFQFYSLLGELTILENI-MLPSLI- 112 Query: 142 DVSAAEAEK-RARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPT 200 A +++K +A L+ VG P A+ YP+ LSGGQ QR+A+ARAL P+I++ DEPT Sbjct: 113 ---AKKSDKTKALELLNLVGFPQNRANNYPSMLSGGQLQRIALARALINSPDIVIADEPT 169 Query: 201 SALDPELVGEVLKVIQTL-AEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEE 252 + LD +++K ++++ E G+T L+ TH A +VL + G+V E Sbjct: 170 ANLDKNSSIDIVKAMRSINKENGQTFLIATHSSEVA-DYCDKVLVISGGQVSE 221 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: 132 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: 276 Length of database: 223 Length adjustment: 24 Effective length of query: 252 Effective length of database: 199 Effective search space: 50148 Effective search space used: 50148 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 Sep 24 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