Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate H281DRAFT_06395 H281DRAFT_06395 amino acid/amide ABC transporter ATP-binding protein 1, HAAT family
Query= uniprot:A0A159ZWS6 (255 letters) >FitnessBrowser__Burk376:H281DRAFT_06395 Length = 255 Score = 174 bits (441), Expect = 2e-48 Identities = 100/253 (39%), Positives = 151/253 (59%), Gaps = 6/253 (2%) Query: 1 MSREILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGG 60 MS IL L R+G A++ V L++ + V ++IGPNGAGKTT+F+ LTG T G Sbjct: 1 MSEAILNASGLVKRYGKFTALSEVNLSIMPRTVHSVIGPNGAGKTTLFHVLTGTLPITAG 60 Query: 61 TILLDGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKT 120 TI+ DG + P H R+GV R+FQ LF +++ ENL +A + +++ + Sbjct: 61 TIVFDGHDVTHEPDHKRVRRGVARSFQVTSLFANLSVQENLRLAA-QGVDSVRALNAWSP 119 Query: 121 PAFRKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEP 180 P + E ++ L+++ L F+ AG L++GQQRRLE+ + RP+ + LDEP Sbjct: 120 PRGALAHTETVDDI---LERLALQRFSKVSAGALSHGQQRRLEVGMALAARPKAIFLDEP 176 Query: 181 AAGLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQ 240 +G+ + +D+K LI LRE++ TV+LIEH+M +VM ISD I V+ QG L +G P++ Sbjct: 177 TSGMGIDDLDDMKQLIRGLREDY--TVVLIEHNMGIVMDISDTITVMQQGRVLVEGRPDE 234 Query: 241 IRDNPEVIKAYLG 253 IR + V AYLG Sbjct: 235 IRGDERVRSAYLG 247 Lambda K H 0.321 0.138 0.398 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: 151 Number of extensions: 5 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: 255 Length of database: 255 Length adjustment: 24 Effective length of query: 231 Effective length of database: 231 Effective search space: 53361 Effective search space used: 53361 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: 47 (22.7 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