Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate 353363 BT3837 ABC transporter ATP-binding protein (NCBI ptt file)
Query= uniprot:A0A159ZWS6 (255 letters) >FitnessBrowser__Btheta:353363 Length = 255 Score = 137 bits (345), Expect = 2e-37 Identities = 82/254 (32%), Positives = 141/254 (55%), Gaps = 16/254 (6%) Query: 2 SREILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGT 61 S+ +L+ E+L ++G V+ V++ VK+ ++V L+GPNGAGKTT F G P G Sbjct: 4 SKMVLRTEDLVKKYGKRTVVSHVSIDVKQGEIVGLLGPNGAGKTTSFYMTVGLITPNEGR 63 Query: 62 ILLDGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTP 121 I LD I P + A+ G+ Q +F+ M+ +N+ TN K Sbjct: 64 IFLDDLEITKFPVYKRAQTGIGYLAQEASVFRQMSVEDNIASVLEM---TN------KPK 114 Query: 122 AFRKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPA 181 ++K + E++ AE+ L KV L+ G++RR EIARC+ P+ +MLDEP Sbjct: 115 DYQKDKLESL-IAEFRLQKVR-----KNKGNQLSGGERRRTEIARCLAIDPKFIMLDEPF 168 Query: 182 AGLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQI 241 AG++P ED++ ++ L+++ N+ +L+ +H+++ +SI+D ++ +G L GTPE++ Sbjct: 169 AGVDPIAVEDIQQIVWKLKDK-NIGILITDHNVQETLSITDRAYLLFEGKILFQGTPEEL 227 Query: 242 RDNPEVIKAYLGEA 255 +N V + YL + Sbjct: 228 AENKIVREKYLSNS 241 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: 171 Number of extensions: 8 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: 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