Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate WP_011384081.1 AMB_RS08460 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_000009985.1:WP_011384081.1 Length = 315 Score = 175 bits (443), Expect = 2e-48 Identities = 101/325 (31%), Positives = 174/325 (53%), Gaps = 24/325 (7%) Query: 85 LTLPTTQRWIVLALIVGALVWPF-FGSRGAVDIATLILIYVMLGLGLNIVVGLAGLLDLG 143 + L T + + AL + + P F + D+ + +L +GLN+++G AG + LG Sbjct: 1 MNLKTARTGGLAALAIVITLAPLGFSNSYFYDVGVNAMFNAILCVGLNLLIGYAGQISLG 60 Query: 144 YVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGF 203 + GF+A+GAY +L+ +G+ L ++ + F++ P+L+L+G YLA+ TLG Sbjct: 61 HAGFFALGAYGSGILTERYGVPAIGALVLSASVVGILAFVVARPILKLKGHYLAMATLGI 120 Query: 204 GEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFERKAAEGLQTFHEYFGLEYNSINKVI 263 G II + L+ ITGGP+G+S F L F K + + Sbjct: 121 GIIIHIVLKTEAGITGGPDGMS---LGNFKMLGFTIKGDQ-------------------M 158 Query: 264 FLYLVALLLALAALFVINRLLRMPIGRAWEALREDEIACRALGLNPTVIKLSAFTLGAAF 323 + ++ +LL LA +N L+ P+GRA A+ E+ +G++ + K+ F + A F Sbjct: 159 WYWVTGVLLVLAVWLSLN-LIESPVGRALRAVHGSEVGAEVVGVDTSSYKVLVFVVSAVF 217 Query: 324 AGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMILLPEMMREF 383 A GS FA + G +TP+ +F S ++ +VVLGGM S G ++ A+++ LLP+++ Sbjct: 218 ASVVGSLFAHKNGFITPDISSFFHSVELVTMVVLGGMASIYGALIGAVILTLLPQVLAAV 277 Query: 384 SEYRMLMFGALMVLMMIWRPQGLLP 408 +Y ++ GA+M+ MI+ P+GLLP Sbjct: 278 EQYEAMILGAIMMGTMIFMPKGLLP 302 Lambda K H 0.331 0.145 0.439 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: 395 Number of extensions: 27 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: 418 Length of database: 315 Length adjustment: 29 Effective length of query: 389 Effective length of database: 286 Effective search space: 111254 Effective search space used: 111254 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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