Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate WP_011384209.1 AMB_RS09130 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_000009985.1:WP_011384209.1 Length = 415 Score = 442 bits (1138), Expect = e-129 Identities = 232/414 (56%), Positives = 298/414 (71%), Gaps = 20/414 (4%) Query: 8 ALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSPAIL---ATIAVCSLLMFLRVLFSTQI 64 AL ++ A+A P+LG++L L + G + ++A LL+ L L Sbjct: 13 ALLGGVVAAAMALPMLGVRLEDGSTGLSLSGRLDWVAWAAGSVAGARLLIGLLRL----- 67 Query: 65 SAMWKSSPGLPVIPAKASNFLTLPTTQRWIVLALIVGALVWPF--FGSRGAVDIATLILI 122 + P LP P ++ W A++ AL+ PF F R VD ATL+LI Sbjct: 68 -GLAGRGPSLPAPPRAMMVYVG------W---AMVAFALILPFLPFSGRNLVDKATLVLI 117 Query: 123 YVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAATFGF 182 YVMLG GLNIVVGLAGLLDLG+V FYAVGAYSYALLS FGLSFW+CLP+AG++AA FG Sbjct: 118 YVMLGWGLNIVVGLAGLLDLGFVAFYAVGAYSYALLSQTFGLSFWVCLPLAGLLAAAFGM 177 Query: 183 LLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFERKAA 242 +LGFPVLRLRGDY+AIVT+G GEI+R+ L+N D+TGGPNGIS IE+P+ FGL+F+ Sbjct: 178 VLGFPVLRLRGDYIAIVTMGLGEIVRVVLQNWQDVTGGPNGISGIERPSLFGLSFKMVPP 237 Query: 243 EGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEIAC 302 EG QTF E+FGL+Y++ ++VIFLY + L LAL + R+ R+P+GRAWEALREDEIAC Sbjct: 238 EGSQTFAEFFGLDYSADHRVIFLYFLILALALLTNVITLRIRRLPVGRAWEALREDEIAC 297 Query: 303 RALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMGS 362 R+LG+NPT++KLSAF GA FAGFAGSFFA RQG ++PESFTFIESA+ILAIVVLGGMGS Sbjct: 298 RSLGINPTLVKLSAFATGAMFAGFAGSFFATRQGFISPESFTFIESAVILAIVVLGGMGS 357 Query: 363 QLGVILAAIVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHMEL 416 Q+G++LAA++++ LPE RE ++RML FG MVL+M+W+P GLL + P + L Sbjct: 358 QIGIVLAALLLVGLPEWFRELQQFRMLAFGGAMVLIMLWKPAGLLSTREPTIRL 411 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: 652 Number of extensions: 36 Number of successful extensions: 1 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: 415 Length adjustment: 31 Effective length of query: 387 Effective length of database: 384 Effective search space: 148608 Effective search space used: 148608 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: 50 (23.9 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