Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_004321583.1 C665_RS15465 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000310185.1:WP_004321583.1 Length = 443 Score = 256 bits (653), Expect = 1e-72 Identities = 159/350 (45%), Positives = 205/350 (58%), Gaps = 48/350 (13%) Query: 9 IIGAVAL---LVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYA 65 ++G VAL + LP++ S V A L+YV+L GLN+VVG AGLLDLGYVAFYA Sbjct: 104 VLGWVALGASIALPIVF-SDNRYVVDTATTVLIYVMLGWGLNVVVGLAGLLDLGYVAFYA 162 Query: 66 VGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRG 125 VGAY +AL+++ S W +PV+ LAA FG +LG P L+LRG Sbjct: 163 VGAYSYALLSTQ----------------FGWSFWEALPVSGALAASFGILLGYPILRLRG 206 Query: 126 DYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLE-------- 177 DYLAIVTLGFGEIIRI L N +NGP G+ I FGLD + Sbjct: 207 DYLAIVTLGFGEIIRIILVNW---TEFSNGPNGISSIPRPSFFGLDFTRSAPEGGQTFAG 263 Query: 178 VFGFD---INSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTR 234 FG + ++ + YYL LVL +++ RL+ +GRAW A+REDEIA +AMG+NT Sbjct: 264 FFGLEFSPMHRLIFLYYLILVLALLTHAFVSRLRKLPVGRAWEALREDEIACQAMGMNTT 323 Query: 235 NMKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGA 294 N+KL AF +GA GG +G F A QGF+SPESF+ ES +I+A+VVLGG+G GV+L A Sbjct: 324 NIKLSAFAIGAMLGGFAGVFFAARQGFISPESFTFTESAIILAIVVLGGMGSQMGVVLAA 383 Query: 295 VLLSALPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGL 344 LL +PE R + A R LL LAM++IM+ RP GL Sbjct: 384 TLLVLIPEFGR--------------NFAEYRMLLFGLAMVLIMVWRPGGL 419 Lambda K H 0.328 0.144 0.430 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: 444 Number of extensions: 25 Number of successful extensions: 4 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: 358 Length of database: 443 Length adjustment: 31 Effective length of query: 327 Effective length of database: 412 Effective search space: 134724 Effective search space used: 134724 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 50 (23.9 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