Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 203044 SO3960 ABC transporter, ATP-binding protein (NCBI ptt file)
Query= TCDB::Q8DQH8 (254 letters) >FitnessBrowser__MR1:203044 Length = 243 Score = 142 bits (359), Expect = 5e-39 Identities = 85/253 (33%), Positives = 142/253 (56%), Gaps = 25/253 (9%) Query: 4 LEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTLD 63 L+ + L K + V DV+L + G++VGL+GPNGAGKTT F ++ G+ + +G + +D Sbjct: 6 LKAQNLAKSYKSRQVVKDVSLTVKTGQVVGLLGPNGAGKTTTFYMVVGLVKSDKGHIFID 65 Query: 64 GHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFYK 123 L + A G+G Q +F+ LTV DN++ A + Sbjct: 66 DDDLTADPMHLRARKGIGYLPQEASIFRKLTVHDNIM-------------------AVLQ 106 Query: 124 SEKEL----KAKALE-LLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEP 178 + KEL + +ALE LL+ F + ++ +LS G++RR+EI RALA PK + LDEP Sbjct: 107 TRKELNSDQREEALEQLLEEFHITHIRDSQGMSLSGGERRRVEIARALAANPKFILLDEP 166 Query: 179 AAGMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDE 238 AG++P ++ ++I ++K + +++ +H++ ++V E Y++ +G LIA+GTP E Sbjct: 167 FAGVDPISVIDIKKIIEQLKSR-GLGVLITDHNVRETLDVCEHAYIVSHGSLIAEGTPAE 225 Query: 239 IKTNKRVIEAYLG 251 I N++V YLG Sbjct: 226 ILDNQQVRAVYLG 238 Lambda K H 0.319 0.139 0.385 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: 146 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: 254 Length of database: 243 Length adjustment: 24 Effective length of query: 230 Effective length of database: 219 Effective search space: 50370 Effective search space used: 50370 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 (21.7 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