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 BWI76_RS07590 BWI76_RS07590 glutamate ABC transporter ATP-binding protein
Query= uniprot:A0A1N7U8S3 (276 letters) >FitnessBrowser__Koxy:BWI76_RS07590 Length = 253 Score = 235 bits (599), Expect = 8e-67 Identities = 127/248 (51%), Positives = 174/248 (70%), Gaps = 8/248 (3%) Query: 27 LQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVITLD 86 + V+ + K++ EVL+ ++L +G V+S++G+SGSGKST+LRC+N+LEQPD G I + Sbjct: 7 VSVKNVSKQFDNVEVLRDINLTVEKGTVVSILGSSGSGKSTLLRCMNWLEQPDRGEIRIS 66 Query: 87 G--ISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLDVS 144 G + I+ GRA + QL +R R+ MVFQ FNLW H+TV +N++ A V + Sbjct: 67 GQRLGIDEHNGRAMSHR----QLSKIRERVGMVFQSFNLWPHLTVQQNVSEALLHVKGMK 122 Query: 145 AAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALD 204 EA+ A L+KVG+ + AD YP LSGGQ+QRVAIAR+LAM PE+ILFDEPTSALD Sbjct: 123 RDEAKAIAMQQLEKVGMAHK-ADVYPITLSGGQKQRVAIARSLAMSPEVILFDEPTSALD 181 Query: 205 PELVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQG-RVEEHGDARILDQPN 263 PELV EVL V++ LA EG TM++VTHEM FARQVS +V+FL +G +E+ + P+ Sbjct: 182 PELVNEVLGVMKALAAEGYTMVVVTHEMDFARQVSDEVVFLEKGLLIEKAPPEKFFSNPD 241 Query: 264 SERLQQFL 271 SER++QFL Sbjct: 242 SERVRQFL 249 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: 211 Number of extensions: 11 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: 253 Length adjustment: 25 Effective length of query: 251 Effective length of database: 228 Effective search space: 57228 Effective search space used: 57228 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