Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate WP_085972724.1 BBTA_RS24910 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_000015165.1:WP_085972724.1 Length = 423 Score = 385 bits (988), Expect = e-111 Identities = 220/422 (52%), Positives = 281/422 (66%), Gaps = 22/422 (5%) Query: 5 LKSALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSPAILATIAVCSLLMFLRVLFS--- 61 LK A+ SAL+ LGL +VG+ E G S + L + +F Sbjct: 2 LKKAVLSALVA-------LGLFSLMVGVRTEA-GQSGQLEYWTRFGELASLVGAVFVGSI 53 Query: 62 -TQISAMWKSSPGL--PVIPAKASNFLTLPTTQRWIVLALIVGALVWP--FFGSRGAVDI 116 ++ +W G +PA + L++ R++ AL++ L+ P F+ R +D+ Sbjct: 54 VVELLRLWLGPRGGLGSFVPASVQSGLSV--AGRYLAPALLIFTLLVPVIFYNQRYILDL 111 Query: 117 ATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMM 176 L+L YVMLG GLN+VVGLAGLLDLGYV FYAVGAYSY LLS FGLSFWICLP+AG++ Sbjct: 112 GILVLTYVMLGWGLNVVVGLAGLLDLGYVAFYAVGAYSYGLLSTTFGLSFWICLPLAGIL 171 Query: 177 AATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLT 236 AA +G LLGFPVLRLRGDYLAIVTL FGEIIRL L N D+TGGPNGIS I +P+ FG+ Sbjct: 172 AAFWGVLLGFPVLRLRGDYLAIVTLAFGEIIRLVLINWQDVTGGPNGISGIPRPSLFGIP 231 Query: 237 FERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALR 296 +GL G+ ++ ++++FL+ + L LAL +V RL R+PIGRAWEALR Sbjct: 232 LT-PGPDGLAAM---LGIPFSPTHRIVFLFYLILALALLTNWVTIRLRRLPIGRAWEALR 287 Query: 297 EDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVV 356 EDE+ACRALG+N T KL+AF GA F GFAG+FFA RQG ++PESFTF ESA++LAIVV Sbjct: 288 EDEVACRALGINITTTKLTAFATGAMFGGFAGAFFATRQGFISPESFTFQESALVLAIVV 347 Query: 357 LGGMGSQLGVILAAIVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHMEL 416 LGGMGSQLGV LAA+ MI E+ R YRML+FG MVL+MIWRP+G++ + P + L Sbjct: 348 LGGMGSQLGVALAALAMIGGFELFRSLEVYRMLVFGLAMVLVMIWRPRGIVGHRSPTVFL 407 Query: 417 RK 418 K Sbjct: 408 EK 409 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: 623 Number of extensions: 33 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: 423 Length adjustment: 32 Effective length of query: 386 Effective length of database: 391 Effective search space: 150926 Effective search space used: 150926 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 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