Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate 3607992 Dshi_1400 ABC transporter related (RefSeq)
Query= CharProtDB::CH_003736 (237 letters) >FitnessBrowser__Dino:3607992 Length = 251 Score = 177 bits (449), Expect = 2e-49 Identities = 97/232 (41%), Positives = 144/232 (62%), Gaps = 5/232 (2%) Query: 6 LSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLC--GDPRATSGRIV 63 LS + A+YG+ + +S ++++GEI+ L+G NGAGKTT L + GDP+ G I Sbjct: 21 LSVWDLHAYYGESYIVQGISFNVHEGEILALLGRNGAGKTTTLRAIARLGDPQVRHGEIW 80 Query: 64 FDDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFAERDQFQERIKWVYEL 123 D + + ++ + + +VPE RR+ +TVEENL + + +R+ Y+L Sbjct: 81 LDHARLHEMESHEAAVAGLGLVPEDRRIIPGLTVEENLQLAQIVEPKGWSLDRL---YDL 137 Query: 124 FPRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQL 183 FPRL ERR Q T+SGGEQQML+I RAL + ++LLLDEP GLAP+I+ +I T+ + Sbjct: 138 FPRLGERRKQEGVTLSGGEQQMLSIARALARDLKVLLLDEPYEGLAPVIVDEIEKTLRVI 197 Query: 184 REQGMTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALLANEAVRSAYL 235 +EQGMT +VEQNA +AL+LADR +L+ G +V +L N +R+ YL Sbjct: 198 KEQGMTTVIVEQNAVRALELADRAVILDTGSIVFDGAAAEVLENAELRAEYL 249 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: 173 Number of extensions: 8 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: 237 Length of database: 251 Length adjustment: 24 Effective length of query: 213 Effective length of database: 227 Effective search space: 48351 Effective search space used: 48351 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