Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate WP_011426558.1 RHE_RS17005 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_000092045.1:WP_011426558.1 Length = 463 Score = 349 bits (896), Expect = e-101 Identities = 212/435 (48%), Positives = 272/435 (62%), Gaps = 38/435 (8%) Query: 5 LKSALFSALLVWAVAYPVLGLKLTIVGINLEV-----HGTSPAILATIAVCSLLMFLRVL 59 L ALF+A+L + +GLK T IN E+ G +A A+ M + + Sbjct: 20 LIEALFAAVLSLGMFVLYVGLK-TDQNINNELIIVQRWGLLAIFVAIAAIGRFAMVVFIK 78 Query: 60 FSTQISAMWKSSPGLPVIPAKASNFLTLPTTQRWIVLALIVGALVWPFF-----GSRGAV 114 + + K+ G I + S F R + ++ L++P G++G++ Sbjct: 79 PNIDRRKLRKAREGDLDISTEKSFF------HRHFLKIALIALLLYPMVIVALVGAQGSL 132 Query: 115 ----DIATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICL 170 + ILIYVML GLNIVVGLAGLLDLGYV FYAVGAYSYALLS YFGLSFW+ L Sbjct: 133 KWVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLL 192 Query: 171 PIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKP 230 P++G++AA +G +LGFPVLRLRGDYLAIVTL FGEIIRL L N TD+T G GIS+I K Sbjct: 193 PLSGILAALWGLILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTRGTFGISSIPKA 252 Query: 231 TFFGLTFERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGR 290 T FG+ F+ A + FH L +S IFL+ + L L + +V RL RMPIGR Sbjct: 253 TLFGIPFDATAGGFAKLFH----LSMSSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGR 308 Query: 291 AWEALREDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAI 350 AWEALREDEIACR+LG+N KL+AF GA F GFAGSFFAARQG V+PESF F+ESA+ Sbjct: 309 AWEALREDEIACRSLGINTVTTKLTAFATGAMFGGFAGSFFAARQGFVSPESFIFLESAV 368 Query: 351 ILAIVVLGGMGSQLGVILAAIVMILLPEMMREF-------------SEYRMLMFGALMVL 397 +LAIVVLGGMGS G+ +AAIVM+ E +RE YRML+FG MV+ Sbjct: 369 VLAIVVLGGMGSLTGIAIAAIVMVGGTEALREMDFLKAVFGPDFTPELYRMLLFGLAMVV 428 Query: 398 MMIWRPQGLLPMQRP 412 +M+++P+G + + P Sbjct: 429 VMLFKPRGFVGSREP 443 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: 631 Number of extensions: 36 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: 418 Length of database: 463 Length adjustment: 32 Effective length of query: 386 Effective length of database: 431 Effective search space: 166366 Effective search space used: 166366 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: 51 (24.3 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