Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate YP_002826585.1 NGR_c20690 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWS6 (255 letters) >NCBI__GCF_000018545.1:YP_002826585.1 Length = 259 Score = 206 bits (523), Expect = 5e-58 Identities = 113/251 (45%), Positives = 162/251 (64%), Gaps = 3/251 (1%) Query: 4 EILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTIL 63 +IL++ L+ RFGGL+AVN V+ +V+E++++++IGPNGAGK+T+F ++ F +PT G + Sbjct: 3 DILEILALTKRFGGLVAVNDVSFSVREREILSVIGPNGAGKSTLFKLISSFLRPTDGEVR 62 Query: 64 LDGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPAF 123 G+ I GL H ARKGVVRTFQ +FK MT +N++ A H + AG + A Sbjct: 63 FKGQRISGLAPHITARKGVVRTFQETTIFKSMTVRDNVVTAHHLRSRAS-LAGFYFGSAA 121 Query: 124 RKSEREAM-EYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAA 182 +S+ EA A+ L + L + A TL +G R L IA + T P +++LDEP A Sbjct: 122 ARSDLEAFGTSADEILTFLGLAPMGSEIASTLPHGHLRALGIAIALATDPSVILLDEPFA 181 Query: 183 GLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIR 242 G+N ET ++ LR E VTVLL+EHDM VM+ISD IVV+N G +A+GTP +I+ Sbjct: 182 GMNHDETRRAVEIVRKLR-ERGVTVLLVEHDMPAVMNISDRIVVLNFGQKIAEGTPAEIQ 240 Query: 243 DNPEVIKAYLG 253 NP+VI+AYLG Sbjct: 241 QNPKVIEAYLG 251 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: 184 Number of extensions: 7 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: 255 Length of database: 259 Length adjustment: 24 Effective length of query: 231 Effective length of database: 235 Effective search space: 54285 Effective search space used: 54285 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 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