Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate GFF2759 HP15_2703 branched-chain amino acid ABC transporter ATP-binding protein
Query= CharProtDB::CH_003736 (237 letters) >FitnessBrowser__Marino:GFF2759 Length = 454 Score = 241 bits (614), Expect = 2e-68 Identities = 122/233 (52%), Positives = 170/233 (72%), Gaps = 1/233 (0%) Query: 5 MLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIVF 64 MLS + YG+I+ LH+V +HIN GEIV+L+GANGAGK+TLL T+ G G I F Sbjct: 221 MLSIKGLVTSYGQIEVLHDVDIHINSGEIVSLVGANGAGKSTLLMTISGLQPTDRGAITF 280 Query: 65 DDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFF-AERDQFQERIKWVYEL 123 + KD++ + + + + VPEGR+VF ++V +NL +G + + + + ++ +Y Sbjct: 281 EGKDLSKITADQRVADGIVQVPEGRQVFKDLSVHDNLLLGAYTRGKTPEVMDDLERMYTK 340 Query: 124 FPRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQL 183 FP L ++R AG +SGG+QQMLA+GRALM+ PRLLLLDEPS+GLAP+II++IF+ +++L Sbjct: 341 FPILRQKRHNLAGELSGGQQQMLAMGRALMAKPRLLLLDEPSMGLAPLIIEEIFNIVKEL 400 Query: 184 REQGMTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALLANEAVRSAYLG 236 +E+G+TIFLVEQNA+QAL LADRGYVLE G VV+ TG LL+NE VR AYLG Sbjct: 401 KEEGITIFLVEQNASQALALADRGYVLETGKVVIEGTGRELLSNEKVREAYLG 453 Lambda K H 0.321 0.137 0.390 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: 284 Number of extensions: 12 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: 237 Length of database: 454 Length adjustment: 28 Effective length of query: 209 Effective length of database: 426 Effective search space: 89034 Effective search space used: 89034 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: 48 (23.1 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