Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate Ga0059261_4235 Ga0059261_4235 ABC-type multidrug transport system, ATPase component
Query= TCDB::P0A9S7 (255 letters) >FitnessBrowser__Korea:Ga0059261_4235 Length = 310 Score = 102 bits (254), Expect = 9e-27 Identities = 76/237 (32%), Positives = 114/237 (48%), Gaps = 23/237 (9%) Query: 6 LSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILLR 65 +SV GL RFG V+ V+LE+ I +GPNG+GKTT + G P GG + Sbjct: 7 ISVEGLTKRFGNRTVVDTVSLEVGRGRICGFLGPNGSGKTTTLRMICGLLIPDGGGGEVL 66 Query: 66 DQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENL-LVAQHQQLKTGLFSGLLKTPSFR 124 L L +++ + + Q LF ++T+ ENL VA L Sbjct: 67 GMDL--LTQRELIKRRIGYMTQRFGLFEDLTIRENLAFVADAYGL--------------- 109 Query: 125 RAQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEPAAGL 184 E + R LER+GL A + A L+ G ++RL +A C++ PEIL+LDEP AG+ Sbjct: 110 ---DEKMKRVDAALERLGLETRAGQLAGTLSGGWKQRLALAACVLHDPEILLLDEPTAGV 166 Query: 185 NPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQI 241 +P +E + + + + TT+L+ H M D Y+ G LA GT ++I Sbjct: 167 DPLARREFWDQV-HMLSAEGTTVLVSTHYMDEAERCHDIAYIA-YGVLLARGTADEI 221 Lambda K H 0.320 0.137 0.395 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: 196 Number of extensions: 6 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: 310 Length adjustment: 26 Effective length of query: 229 Effective length of database: 284 Effective search space: 65036 Effective search space used: 65036 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