Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate WP_041277992.1 DP_RS12580 ABC transporter ATP-binding protein
Query= CharProtDB::CH_003736 (237 letters) >NCBI__GCF_000025945.1:WP_041277992.1 Length = 241 Score = 238 bits (606), Expect = 1e-67 Identities = 123/234 (52%), Positives = 167/234 (71%), Gaps = 1/234 (0%) Query: 3 KVMLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRI 62 + +L+ + YG I A+ +SL +++GEIVT++G+NGAGKTT + T+ RA SG I Sbjct: 5 EALLNITDLEVSYGNIAAIKGISLQVHRGEIVTILGSNGAGKTTTMRTITQLLRAKSGSI 64 Query: 63 VFDDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFAERDQFQERIKWVYE 122 +FD ++T KI+ ++ PEGRRVF +TVEENL +G + +++ E + WVY Sbjct: 65 IFDGVELTQLPAHKIVSLGMSHSPEGRRVFGILTVEENLLLGAY-SKKKMDPEILGWVYN 123 Query: 123 LFPRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQ 182 LFPRL ERR Q AGT+SGGEQQMLAIGRALMS P +LLLDEPSLG+API+++ IF I++ Sbjct: 124 LFPRLEERRSQLAGTLSGGEQQMLAIGRALMSKPSMLLLDEPSLGIAPILVKAIFAQIKK 183 Query: 183 LREQGMTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALLANEAVRSAYLG 236 + E G+T+ LVEQNA AL+LA+RGY+LE G +V S T LLA+ V+ AYLG Sbjct: 184 IAESGVTVLLVEQNAKAALRLANRGYILEVGKIVFSGTSAELLASPKVQEAYLG 237 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: 156 Number of extensions: 4 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: 241 Length adjustment: 23 Effective length of query: 214 Effective length of database: 218 Effective search space: 46652 Effective search space used: 46652 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 24 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