Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_011385357.1 AMB_RS15010 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >NCBI__GCF_000009985.1:WP_011385357.1 Length = 366 Score = 183 bits (464), Expect = 7e-51 Identities = 117/361 (32%), Positives = 178/361 (49%), Gaps = 12/361 (3%) Query: 13 IAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKKIKFE 72 +AAA +A A + IG P+SG++A +G+ + GA A+E++NA+G +G K Sbjct: 11 LAAALLMAGAARADITIGVAGPLSGSEAAFGEQFKRGAMKAVEDINAKGGVLGQK---LA 67 Query: 73 LVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAATNPN 132 L DDA DPKQ A A ++ KV V GH SG++IPAS+VY + GI ++ A+TNP Sbjct: 68 LTLGDDACDPKQAVAVANEMAAKKVPFVAGHFCSGSSIPASEVYAETGILQISPASTNPK 127 Query: 133 LTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKKTATAK 192 T+ G FR D+ G A Y K K VAI+ D++AYG+G+AD + Sbjct: 128 FTERGLPNIFRTCGRDDQQGVIAADYIAKHQKDKVVAIVHDKSAYGKGLADQTRDALGKA 187 Query: 193 GMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNVKYFG 252 G+K + + D+ A++T +KA D +++GG + G ++RQ+ GM + G Sbjct: 188 GIKAALYEAISAGEKDYSALVTKLKASKVDLLYFGGYKTEAGLIVRQLRDQGM-QTRLMG 246 Query: 253 GDGICTSEIAKL--AAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQVYSPY 310 GD + T E + AAG T+ S + A KY + + Y+ Y Sbjct: 247 GDALVTEEYWAITGAAGEGTMMTF------SPDPRKNPANADLVKYYRAQKYEPEAYTLY 300 Query: 311 TYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITLYVYKDG 370 TY A ++A + D K L F I F+ G++ P +YV+K G Sbjct: 301 TYGTIQAWAQAAEKAKTTDWKKVAAVLKAEKFDTAIGKIGFDAKGDVAAPGYVMYVWKGG 360 Query: 371 K 371 K Sbjct: 361 K 361 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: 382 Number of extensions: 14 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: 366 Length adjustment: 30 Effective length of query: 345 Effective length of database: 336 Effective search space: 115920 Effective search space used: 115920 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: 49 (23.5 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