Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate RR42_RS29450 RR42_RS29450 ABC transporter
Query= uniprot:A0A159ZWS6 (255 letters) >FitnessBrowser__Cup4G11:RR42_RS29450 Length = 265 Score = 235 bits (599), Expect = 8e-67 Identities = 117/253 (46%), Positives = 170/253 (67%) Query: 1 MSREILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGG 60 M+ +L V +LS+RFGG+LA+ GV+ V+ +V LIGPNGAGKTTVFN ++ Y PT G Sbjct: 1 MTDTLLSVRDLSVRFGGVLALGGVSFDVRRGEVFTLIGPNGAGKTTVFNLISRIYPPTSG 60 Query: 61 TILLDGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKT 120 IL G + LP H IA +G+ RTFQN+ LF+ T ++NLLI H H + F+A L T Sbjct: 61 EILWQGSSLTRLPPHAIAAQGIARTFQNIELFEHATVLQNLLIGHHTHRASGFWADLLFT 120 Query: 121 PAFRKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEP 180 PA R+SE A AE ++ ++L + L YG ++ +E+AR + + PR+L+LDEP Sbjct: 121 PAARRSELAARHKAEEMIELLDLQAHRDALVAGLPYGVRKVVELARALCSSPRLLLLDEP 180 Query: 181 AAGLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQ 240 ++GLN +ETED+ I ++ E +TVL++EHDM LV +SD ++ +NQG LA GTP + Sbjct: 181 SSGLNVEETEDMAWWIRDIQSELGITVLMVEHDMSLVSRVSDRVLAMNQGQVLAQGTPAE 240 Query: 241 IRDNPEVIKAYLG 253 ++++P VI+AYLG Sbjct: 241 VQEHPGVIEAYLG 253 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: 192 Number of extensions: 3 Number of successful extensions: 1 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: 265 Length adjustment: 24 Effective length of query: 231 Effective length of database: 241 Effective search space: 55671 Effective search space used: 55671 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