Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate SMc01946 SMc01946 leucine-specific binding protein
Query= uniprot:A0A165KTD4 (375 letters) >FitnessBrowser__Smeli:SMc01946 Length = 372 Score = 184 bits (468), Expect = 3e-51 Identities = 122/367 (33%), Positives = 183/367 (49%), Gaps = 12/367 (3%) Query: 5 LKLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTI 64 L + A+ A +G A A + +G P++G A +G + GA A E++NA G I Sbjct: 6 LSAVALTAMVAFSGTAWAD---ILVGVGGPLTGPNAAFGAQLQKGAEQAAEDINAAG-GI 61 Query: 65 GGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHV 124 G++IK +V DD +DPKQG + AQK V VVGH NSG +IPAS++Y + GI V Sbjct: 62 NGEQIK--VVLGDDVSDPKQGVSVAQKFVADGVKFVVGHFNSGVSIPASEIYAENGILQV 119 Query: 125 TGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADV 184 T A+TNP T+ G TFR D+ GA Y K VA+I D+T YGQG+AD Sbjct: 120 TPASTNPQFTERGLWNTFRTCGRDDQQGAVAGAYIAANFKDAKVAVIHDKTPYGQGLADE 179 Query: 185 FKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLG 244 KK+ G+ + DF A++ +K ++YGG+ + G ++RQM+ G Sbjct: 180 TKKSMNEAGVTEALYEGINTGDKDFSALIAKMKQAGVSIVYYGGLHTEAGLIMRQMKDQG 239 Query: 245 MGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQF 304 + GDGI ++E+A +A A G ++ K P K+ A + Sbjct: 240 L-KATMMSGDGIVSNELASIAGDAVD-GTLMTF--APDPRKSPAAKDLVEKFRAA-GFEP 294 Query: 305 QVYSPYTYDATFLIVDAMKRANSVDPKVYTPEL-AKSSFKGVTSTIAFEPNGEMKNPAIT 363 + Y+ Y Y A +I + K A + DP+ + AK FK + F+ G++ P Sbjct: 295 EAYTLYAYAALQVIAEGAKAAGNTDPQAVAEAIKAKGPFKTAIGELGFDEKGDITRPDYV 354 Query: 364 LYVYKDG 370 +Y +K G Sbjct: 355 MYTWKKG 361 Lambda K H 0.315 0.131 0.375 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: 409 Number of extensions: 23 Number of successful extensions: 5 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: 375 Length of database: 372 Length adjustment: 30 Effective length of query: 345 Effective length of database: 342 Effective search space: 117990 Effective search space used: 117990 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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