Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate 206141 DVU0716 branched-chain amino acid ABC transporter, ATP-binding protein
Query= CharProtDB::CH_003736 (237 letters) >MicrobesOnline__882:206141 Length = 238 Score = 239 bits (611), Expect = 3e-68 Identities = 117/235 (49%), Positives = 168/235 (71%), Gaps = 1/235 (0%) Query: 4 VMLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIV 63 + L + YG ++ALH + + +++GEIVT++GANGAGKTT L ++ G + + G + Sbjct: 1 MFLELRNLHVKYGNVEALHGIDIRVDEGEIVTILGANGAGKTTTLMSISGLVKPSEGGVF 60 Query: 64 FDDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFA-ERDQFQERIKWVYE 122 F D+ + + +++ + PEGRRVF ++V ENL +G F ++ + + + W++E Sbjct: 61 FRDEPLHKLHSHEVVARGITQSPEGRRVFGTLSVLENLYLGAFTCRDKARVERTLGWIFE 120 Query: 123 LFPRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQ 182 LFPRL ERR Q AGT+SGGEQQMLAIGRALM +P++LLLDEPSLGLAPI+++ IFDT+ Sbjct: 121 LFPRLEERRGQLAGTLSGGEQQMLAIGRALMGDPKVLLLDEPSLGLAPILVKSIFDTVRT 180 Query: 183 LREQGMTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALLANEAVRSAYLGG 237 + + G+T+ LVEQNA ALKLA RGYV+E G VV+ D+ +LLAN V++AYLGG Sbjct: 181 INQSGVTVVLVEQNARAALKLATRGYVMEVGRVVMEDSAASLLANPEVQAAYLGG 235 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: 189 Number of extensions: 6 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: 238 Length adjustment: 23 Effective length of query: 214 Effective length of database: 215 Effective search space: 46010 Effective search space used: 46010 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