Align NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate WP_086510701.1 BZY95_RS14925 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8YXD0 (288 letters) >NCBI__GCF_002151265.1:WP_086510701.1 Length = 335 Score = 174 bits (442), Expect = 2e-48 Identities = 100/326 (30%), Positives = 174/326 (53%), Gaps = 51/326 (15%) Query: 8 LIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVN------------ 55 +I+ G GSI A+ A+G+TL + I+R ++FAH D +T GA++ + Sbjct: 11 VIIAGSVTGSIYAIGAIGVTLIFSIMRFAHFAHADMMTFGAFMVLLLTLAFPGVGGVVGL 70 Query: 56 -TFGVNIWLSMIVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIIL 114 T V + L+MI+ VG+ +K+ + +R+ ++I S+G+ L L+ I L Sbjct: 71 PTPIVMLPLAMILTAALAVGI----DKVFYKPLRAHGVKPIVIVIGSLGVTLMLQGLIRL 126 Query: 115 IWGGRNQN----------YNLPITPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTK 164 G QN Y L + L + V + Q+++ L + + LH L T+ Sbjct: 127 FAGTSAQNMYLAGERKEIYRLDVPFELATRPIIVTEPQIILFILTIACVVGLHVFLNRTR 186 Query: 165 IGKAMRAVADDLDLAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLIL 224 +GKAMRA++D+ DLA+ SGI+ ++ TW+IAG++ ++ G++ L +P++ +FL+L Sbjct: 187 LGKAMRAMSDNPDLARASGINTNYIVSVTWVIAGSLAAIAGTLLSLDVTFKPDLSFFLLL 246 Query: 225 PLFASVILGGIGNPYGAIAAAFIIGIVQEVST------------------------PFLG 260 P+FA+ I+GG+G+PYGAIA F++G + ++ F+G Sbjct: 247 PIFAAAIVGGVGHPYGAIAGGFVVGFAETLAVFNWAVLLRPIAHLFPEWIEIPRNLAFVG 306 Query: 261 SQYKQGVALLIMILVLLIRPKGLFKG 286 ++YK V I++ +L+ RP G+FKG Sbjct: 307 TEYKIVVPFFILVAILVWRPTGIFKG 332 Lambda K H 0.328 0.144 0.426 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: 280 Number of extensions: 21 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: 288 Length of database: 335 Length adjustment: 27 Effective length of query: 261 Effective length of database: 308 Effective search space: 80388 Effective search space used: 80388 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 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