Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate 203044 SO3960 ABC transporter, ATP-binding protein (NCBI ptt file)
Query= CharProtDB::CH_003736 (237 letters) >FitnessBrowser__MR1:203044 Length = 243 Score = 134 bits (337), Expect = 2e-36 Identities = 76/240 (31%), Positives = 131/240 (54%), Gaps = 6/240 (2%) Query: 1 MEKVMLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSG 60 M ++ L ++ Y Q + +VSL + G++V L+G NGAGKTT + G ++ G Sbjct: 1 MTQITLKAQNLAKSYKSRQVVKDVSLTVKTGQVVGLLGPNGAGKTTTFYMVVGLVKSDKG 60 Query: 61 RIVFDDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFAER----DQFQER 116 I DD D+T R+ + +P+ +F ++TV +N+ M + DQ +E Sbjct: 61 HIFIDDDDLTADPMHLRARKGIGYLPQEASIFRKLTVHDNI-MAVLQTRKELNSDQREEA 119 Query: 117 IKWVYELFPRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQI 176 ++ + E F H R Q ++SGGE++ + I RAL +NP+ +LLDEP G+ PI + I Sbjct: 120 LEQLLEEFHITHIRDSQGM-SLSGGERRRVEIARALAANPKFILLDEPFAGVDPISVIDI 178 Query: 177 FDTIEQLREQGMTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALLANEAVRSAYLG 236 IEQL+ +G+ + + + N + L + + Y++ +G ++ T +L N+ VR+ YLG Sbjct: 179 KKIIEQLKSRGLGVLITDHNVRETLDVCEHAYIVSHGSLIAEGTPAEILDNQQVRAVYLG 238 Lambda K H 0.321 0.137 0.390 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: 105 Number of extensions: 3 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: 237 Length of database: 243 Length adjustment: 23 Effective length of query: 214 Effective length of database: 220 Effective search space: 47080 Effective search space used: 47080 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