Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate WP_027457108.1 K420_RS0105080 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWL6 (233 letters) >NCBI__GCF_000519045.1:WP_027457108.1 Length = 251 Score = 231 bits (589), Expect = 1e-65 Identities = 124/236 (52%), Positives = 166/236 (70%), Gaps = 5/236 (2%) Query: 1 MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY 60 +L +N+ YGK++ALH V++ +R+GEIVT+IG NGAGK+TLL L G ++ G I Y Sbjct: 12 ILDVKNLRVAYGKVEALHEVSLTIRRGEIVTVIGPNGAGKTTLLSALMGLLPSN-GDIVY 70 Query: 61 MGEELVGQDS-SHIMRKSIAVVPEGRRVFARLTVEENLAMGGFF---TDKGDYQEQMDKV 116 MG+ + S H++R + +VPE R +FA ++VE+NL +G F T D E MD+V Sbjct: 71 MGQLQKHERSVEHLVRHGMTLVPEKRELFAEMSVEDNLLLGAFDRYRTGHRDEMETMDEV 130 Query: 117 LHLFPRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDII 176 LFPRL+ER Q GT+SGGE+QMLA+GRALM+KPKLL+LDEPSLGLAP+II++IF I Sbjct: 131 FELFPRLEERRAQLAGTLSGGERQMLAMGRALMAKPKLLMLDEPSLGLAPLIIKEIFRTI 190 Query: 177 EQLRKDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLG 232 L++ GV + LVEQNA AL+I+D YVLE G + + G L DP+V EAYLG Sbjct: 191 SALKETGVAILLVEQNARAALQISDYGYVLETGEIKLSGPSAELAADPRVIEAYLG 246 Lambda K H 0.320 0.137 0.381 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: 233 Length of database: 251 Length adjustment: 23 Effective length of query: 210 Effective length of database: 228 Effective search space: 47880 Effective search space used: 47880 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