Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_012335132.1 M446_RS26235 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >NCBI__GCF_000019365.1:WP_012335132.1 Length = 372 Score = 200 bits (508), Expect = 6e-56 Identities = 132/361 (36%), Positives = 188/361 (52%), Gaps = 12/361 (3%) Query: 9 VVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKK 68 VVAA A AG A AQ +KI P++GA A +G +NGA A+E++N G +G K Sbjct: 7 VVAAGLAFAGSAQAQ---IKIAVAGPITGANAAFGAQLKNGAVQAVEDINKAGGILGQKI 63 Query: 69 IKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAA 128 + LV DDA+DPKQG + A K V VVGH NSG +IPAS+VY + GI +T A+ Sbjct: 64 V---LVDGDDASDPKQGVSVANKFAAEGVKAVVGHFNSGVSIPASEVYAESGIVQITPAS 120 Query: 129 TNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKKT 188 TNP T TFR D+ GA Y K K VA + D+T YG+G+AD K Sbjct: 121 TNPKFTDRKLWNTFRTCGRDDQQGAVAGAYLASHFKGKNVAFVHDKTPYGRGLADETLKA 180 Query: 189 ATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNV 248 AKG K V + D+ A+++ +K D +++GG+ P+ G ++RQM G+ NV Sbjct: 181 LKAKGGKDVLFEGINPGEKDYSALVSKLKQAKTDVVYFGGLHPEAGLIVRQMHDQGL-NV 239 Query: 249 KYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQVYS 308 GDGI E A++ AG G ++ K P A + AK + + Y+ Sbjct: 240 PLMSGDGITDKEFAQI-AGPGADGTLMTF--SPDARKNPNAKDVVAAFKAKNIDP-EAYT 295 Query: 309 PYTYDATFLIVDAMKRANSVDPKVYTPEL-AKSSFKGVTSTIAFEPNGEMKNPAITLYVY 367 Y+Y A ++ AM+ A S D K + + FK V IA++ G++ P +YV+ Sbjct: 296 LYSYAAFQILKAAMEEAKSTDSKKVAEIMHSGKPFKTVIGDIAYDKKGDITRPDYVMYVW 355 Query: 368 K 368 K Sbjct: 356 K 356 Lambda K H 0.315 0.131 0.375 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: 413 Number of extensions: 18 Number of successful extensions: 3 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: 375 Length of database: 372 Length adjustment: 30 Effective length of query: 345 Effective length of database: 342 Effective search space: 117990 Effective search space used: 117990 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 50 (23.9 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