Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate AZOBR_RS32400 AZOBR_RS32400 leucine/isoleucine/valine transporter ATP-binding subunit
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__azobra:AZOBR_RS32400 Length = 232 Score = 224 bits (571), Expect = 1e-63 Identities = 122/235 (51%), Positives = 166/235 (70%), Gaps = 4/235 (1%) Query: 11 LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70 +L+V + G L GV + V +G IV+++GANG GK+TLM + G + G+ VF Sbjct: 1 ILEVRDLTVRMGPQEILRGVSLDVAEGAIVAVLGANGVGKTTLMRALSGIYRTSGGATVF 60 Query: 71 EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKH-FAEDVEKIFTL 129 +G D+T P+HE+ R +AQ+PEGR+IF MTV ENL +G L+H A +E++ L Sbjct: 61 DGEDMTDSPSHEVVRRGLAQAPEGRQIFGTMTVRENLLLGG--RTLRHDRAARMERMLEL 118 Query: 130 FPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKL 189 FPRL+ER Q+ G+LSGGEQQML I RALM++P+LLLLDEPSLGLAP++VK IF+ + ++ Sbjct: 119 FPRLRERLIQKAGSLSGGEQQMLCIARALMSKPRLLLLDEPSLGLAPMVVKQIFDLLVQI 178 Query: 190 NEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYLEG 244 EG ++ LVEQNA AALR++ AYVM G+VT+SGS +L A+P VRAAYL G Sbjct: 179 -RGEGTSILLVEQNARAALRVADHAYVMEAGRVTLSGSAADLAADPRVRAAYLGG 232 Lambda K H 0.320 0.137 0.387 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: 204 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: 247 Length of database: 232 Length adjustment: 23 Effective length of query: 224 Effective length of database: 209 Effective search space: 46816 Effective search space used: 46816 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 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