Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate WP_011767164.1 AZO_RS17290 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWL6 (233 letters) >NCBI__GCF_000061505.1:WP_011767164.1 Length = 280 Score = 197 bits (500), Expect = 2e-55 Identities = 108/240 (45%), Positives = 152/240 (63%), Gaps = 9/240 (3%) Query: 2 LQFENVSTFYGK-IQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAH-----S 55 L NV Y I L V++EV QG IV L+GANGAGKST L ++ +A Sbjct: 18 LSINNVEVIYDHVILVLKGVSLEVPQGSIVALLGANGAGKSTTLKSISNLLRAERGDVTK 77 Query: 56 GSIRYMGEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTD--KGDYQEQM 113 GSI + G + + ++++ + V EGR F LT+EENL G + + + ++ + Sbjct: 78 GSIEFKGARVDQMTPNELVKRGVIQVMEGRHCFGHLTIEENLLTGAYTRSISRAELKDNL 137 Query: 114 DKVLHLFPRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIF 173 +KV H FPRLK R T + G SGGEQQM AIGRALM+KP+++LLDEPS+GLAP I+++IF Sbjct: 138 EKVYHYFPRLKTRRTSQAGYTSGGEQQMCAIGRALMAKPEMILLDEPSMGLAPQIVEEIF 197 Query: 174 DIIEQLR-KDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLG 232 +I++ L K+ V+ L EQN AL+ AD Y++ENGR+VM+G + L T+ V+E YLG Sbjct: 198 EIVKDLNSKERVSFLLAEQNTMVALRYADFGYIMENGRIVMEGAAKDLATNEDVKEFYLG 257 Lambda K H 0.320 0.137 0.381 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: 159 Number of extensions: 6 Number of successful extensions: 4 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: 233 Length of database: 280 Length adjustment: 24 Effective length of query: 209 Effective length of database: 256 Effective search space: 53504 Effective search space used: 53504 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 24 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