Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF250 PGA1_c02620 high-affinity branched-chain amino acid transport ATP-binding protein LivF
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__Phaeo:GFF250 Length = 257 Score = 216 bits (551), Expect = 3e-61 Identities = 113/236 (47%), Positives = 154/236 (65%), Gaps = 1/236 (0%) Query: 8 GQPLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGS 67 G LL + +E++YG I A+ GV + V G+IV+++GANGAGKSTL+ TI G GS Sbjct: 2 GAALLDIRNLESFYGPIMAIRGVSLSVQAGQIVTVLGANGAGKSTLLKTISGIMDPEKGS 61 Query: 68 VVFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLD-NLKHFAEDVEKI 126 V F G +I H I R I PEGR +FP ++V ENL +GA + D + + Sbjct: 62 VSFNGEEIQGEEPHRIVRRGIVHVPEGREVFPLLSVEENLTLGAYTRRDQAEIERDRQMV 121 Query: 127 FTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAI 186 F FP L ER Q GTLSGG+QQML+IGR LM RP+++LLDEPSLGL+PL+V+ IF + Sbjct: 122 FDYFPILAERRHQEAGTLSGGQQQMLAIGRGLMLRPRIMLLDEPSLGLSPLLVQEIFGIL 181 Query: 187 RKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242 ++LN EG+T+ LVEQNA AL L+H YVM G++ M GS L+ + ++++ YL Sbjct: 182 KRLNRDEGVTMMLVEQNARIALELAHVGYVMEIGRIVMDGSADRLMESEDIKSFYL 237 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: 189 Number of extensions: 5 Number of successful extensions: 2 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: 257 Length adjustment: 24 Effective length of query: 223 Effective length of database: 233 Effective search space: 51959 Effective search space used: 51959 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