Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate 353363 BT3837 ABC transporter ATP-binding protein (NCBI ptt file)
Query= CharProtDB::CH_003736 (237 letters) >FitnessBrowser__Btheta:353363 Length = 255 Score = 129 bits (324), Expect = 5e-35 Identities = 74/235 (31%), Positives = 127/235 (54%), Gaps = 3/235 (1%) Query: 3 KVMLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRI 62 K++L + + YGK + VS+ + QGEIV L+G NGAGKTT G GRI Sbjct: 5 KMVLRTEDLVKKYGKRTVVSHVSIDVKQGEIVGLLGPNGAGKTTSFYMTVGLITPNEGRI 64 Query: 63 VFDDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLA--MGGFFAERDQFQERIKWV 120 DD +IT + K + + + + VF +M+VE+N+A + +D +++++ + Sbjct: 65 FLDDLEITKFPVYKRAQTGIGYLAQEASVFRQMSVEDNIASVLEMTNKPKDYQKDKLESL 124 Query: 121 YELFPRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTI 180 F RL + R + +SGGE++ I R L +P+ ++LDEP G+ PI ++ I + Sbjct: 125 IAEF-RLQKVRKNKGNQLSGGERRRTEIARCLAIDPKFIMLDEPFAGVDPIAVEDIQQIV 183 Query: 181 EQLREQGMTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALLANEAVRSAYL 235 +L+++ + I + + N + L + DR Y+L G ++ T + L N+ VR YL Sbjct: 184 WKLKDKNIGILITDHNVQETLSITDRAYLLFEGKILFQGTPEELAENKIVREKYL 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: 119 Number of extensions: 5 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: 255 Length adjustment: 24 Effective length of query: 213 Effective length of database: 231 Effective search space: 49203 Effective search space used: 49203 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