Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate Ac3H11_3213 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)
Query= CharProtDB::CH_003736 (237 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3213 Length = 236 Score = 198 bits (504), Expect = 7e-56 Identities = 107/237 (45%), Positives = 149/237 (62%), Gaps = 4/237 (1%) Query: 1 MEKVMLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGD-PRATS 59 M L+ ++ Y Q L ++SL G I ++G NGAGKTTLL L G PR + Sbjct: 1 MSGAHLTVQNLTTGYHGFQVLQDLSLQAAPG-ITVIVGPNGAGKTTLLKALAGLLPR--T 57 Query: 60 GRIVFDDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFAERDQFQERIKW 119 G + D D+ ++ +A+V EGR++F +MTV ENL +GG+ +R+ Sbjct: 58 GTVALDGSDLPAMNATACVQRGLALVAEGRQLFPQMTVTENLELGGWLVPSRTRADRLAQ 117 Query: 120 VYELFPRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDT 179 +E FPRL ER Q AGTMSGGEQQM+A+ RALMS PRLL+LDEPSLGLAP ++ ++ Sbjct: 118 AFEDFPRLKERATQLAGTMSGGEQQMVAVARALMSGPRLLMLDEPSLGLAPRMVDELLAI 177 Query: 180 IEQLREQGMTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALLANEAVRSAYLG 236 ++++ QG+T+ +VEQN +AL++A RGYVLE G +V S LL ++ VR AYLG Sbjct: 178 VQRIAAQGVTVLMVEQNVRKALQIAQRGYVLERGRIVASGAASDLLQSDVVRQAYLG 234 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: 149 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: 237 Length of database: 236 Length adjustment: 23 Effective length of query: 214 Effective length of database: 213 Effective search space: 45582 Effective search space used: 45582 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