Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate PfGW456L13_120 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)
Query= uniprot:A0A159ZWS6 (255 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_120 Length = 238 Score = 124 bits (311), Expect = 2e-33 Identities = 84/255 (32%), Positives = 135/255 (52%), Gaps = 21/255 (8%) Query: 1 MSREILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGG 60 MS+ IL+++ L + +G + A+ GV+L + E + V+LIG NGAGK+T+ + G + G Sbjct: 1 MSKPILELKELDVFYGPIQALKGVSLHINEGETVSLIGSNGAGKSTLLMSIFGQPRAADG 60 Query: 61 TILLDGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKT 120 IL G I H+IA G+ ++ + R+F DMT ENLL+ Sbjct: 61 QILYQGVDITHKSSHYIASNGIAQSPEGRRVFPDMTVEENLLMG--------------TI 106 Query: 121 PAFRKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEP 180 P K +E M+ + L E + A T++ G+Q+ L IAR +M+RP++L+LDEP Sbjct: 107 PIGDKYAKEDMQRMFELFPR--LEERRTQRAMTMSGGEQQMLAIARALMSRPKLLLLDEP 164 Query: 181 AAGLNPKETEDLKALIGVLRE--EHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTP 238 + GL P +K + LRE + +T+ L+E + + +SD V+ G GT Sbjct: 165 SLGLAPIV---VKQIFATLRELAKTGMTIFLVEQNANHALRLSDRAYVMVNGEIRMTGTG 221 Query: 239 EQIRDNPEVIKAYLG 253 +++ N +V AYLG Sbjct: 222 KELLVNEDVRSAYLG 236 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: 159 Number of extensions: 9 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: 238 Length adjustment: 24 Effective length of query: 231 Effective length of database: 214 Effective search space: 49434 Effective search space used: 49434 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: 46 (22.3 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