Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate WP_012591091.1 MSIL_RS10640 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_000021745.1:WP_012591091.1 Length = 456 Score = 348 bits (893), Expect = e-100 Identities = 203/435 (46%), Positives = 274/435 (62%), Gaps = 31/435 (7%) Query: 5 LKSALFSALLVWAVAYPVLGLKLTIVGINLEVHGTS--PAILATIAVCSLLMFLRVLFST 62 L A + +++ + +P+L + T + E++ S PA+ + +L F ++ Sbjct: 18 LTGAAIAGAIMFGLCFPILAFR-TDQNFSNELYLLSRWPAVAFAVGAVFVLRFAMLMLPP 76 Query: 63 QISAMWKSSPGLPVIPAKASNFLTLPTTQ------RWIVLALIVGALVWPFFGSRGAVDI 116 + + P P PA+A L I L++ AL+ P + + Sbjct: 77 R-----EPRPQAPPSPARAGALQRLARYAGAVGILALIAFPLVMVALLGPAGAQKWIDNF 131 Query: 117 ATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMM 176 IL+YV+LG GLNIVVGLAGLLDLGYV FYAVGAY+YALL+ +FG SFW+CLP+AG++ Sbjct: 132 GVQILLYVLLGWGLNIVVGLAGLLDLGYVAFYAVGAYAYALLATHFGWSFWLCLPVAGLL 191 Query: 177 AATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLT 236 AA FG LG PVLRLRGDYLAIVT+ FGEIIRL L N T +T G GIS+I + TFFG Sbjct: 192 AAGFGVALGLPVLRLRGDYLAIVTMAFGEIIRLVLTNWTALTNGDAGISSIPRITFFGWP 251 Query: 237 FERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALR 296 F G F FGL++ ++++IFL+ + L LAL ++ RL + P+GRA+EALR Sbjct: 252 F----IAGPNGFAALFGLKFAPVHRLIFLFYLILALALCVNYLTRRLRKAPLGRAFEALR 307 Query: 297 EDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVV 356 EDEIACR+LG++ KL+AF LGA+ AG AG+ FAARQ V+P SFTF+ESA ILA+VV Sbjct: 308 EDEIACRSLGVDTVATKLTAFALGASIAGMAGALFAARQNFVSPTSFTFMESATILALVV 367 Query: 357 LGGMGSQLGVILAAIVMILLPEMMREF-------------SEYRMLMFGALMVLMMIWRP 403 LGG GSQLGV LAAIV+I E++RE ++YRML+ G MV MM WRP Sbjct: 368 LGGAGSQLGVALAAIVIIGGSEILRELDGLKQIFGPAFDPTQYRMLIVGIAMVGMMNWRP 427 Query: 404 QGLLPMQRPHMELRK 418 +GL+ ++ P + L+K Sbjct: 428 RGLIALRTPSIFLKK 442 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: 616 Number of extensions: 33 Number of successful extensions: 4 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: 456 Length adjustment: 32 Effective length of query: 386 Effective length of database: 424 Effective search space: 163664 Effective search space used: 163664 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