Align Solute-binding (Aliphatic amino acid) component of ABC transporter (characterized, see rationale)
to candidate SMc01946 SMc01946 leucine-specific binding protein
Query= uniprot:Q1MDE9 (367 letters) >FitnessBrowser__Smeli:SMc01946 Length = 372 Score = 336 bits (861), Expect = 7e-97 Identities = 168/352 (47%), Positives = 230/352 (65%), Gaps = 1/352 (0%) Query: 10 LVASLAFAPLAHADITIGLIAPLTGPVAAYGDQVKNGAQTAVDEINKKGGILGEKVVLEL 69 L A +AF+ A ADI +G+ PLTGP AA+G Q++ GA+ A ++IN GGI GE++ + L Sbjct: 11 LTAMVAFSGTAWADILVGVGGPLTGPNAAFGAQLQKGAEQAAEDINAAGGINGEQIKVVL 70 Query: 70 ADDAGEPKQGVSAANKVVGDGIRFVVGPVTSGVAIPVSDVLAENGVLMVTPTATAPDLTK 129 DD +PKQGVS A K V DG++FVVG SGV+IP S++ AENG+L VTP +T P T+ Sbjct: 71 GDDVSDPKQGVSVAQKFVADGVKFVVGHFNSGVSIPASEIYAENGILQVTPASTNPQFTE 130 Query: 130 RGLTNVLRTCGRDDQQAEVAAKYVLKNFKDKRVAIVNDKGAYGKGLADAFKATLNAGGIT 189 RGL N RTCGRDDQQ VA Y+ NFKD +VA+++DK YG+GLAD K ++N G+T Sbjct: 131 RGLWNTFRTCGRDDQQGAVAGAYIAANFKDAKVAVIHDKTPYGQGLADETKKSMNEAGVT 190 Query: 190 EVVNDAITPGDKDFSALTTRIKSEKVDVVYFGGYHPEGGLLARQLHDLAANATIIGGDGL 249 E + + I GDKDFSAL ++K V +VY+GG H E GL+ RQ+ D AT++ GDG+ Sbjct: 191 EALYEGINTGDKDFSALIAKMKQAGVSIVYYGGLHTEAGLIMRQMKDQGLKATMMSGDGI 250 Query: 250 SNTEFWAIGTDAAGGTIFTNASDATKSPDSKAAADALAAKNIPAEAFTLNAYAAVEVLKA 309 + E +I DA GT+ T A D KSP +K + A EA+TL AYAA++V+ Sbjct: 251 VSNELASIAGDAVDGTLMTFAPDPRKSPAAKDLVEKFRAAGFEPEAYTLYAYAALQVIAE 310 Query: 310 GIEKAGSAEDAEAVATALKDGKEIPTAIGKVTYGETGDLTSQSFSLYKWEAG 361 G + AG+ D +AVA A+K TAIG++ + E GD+T + +Y W+ G Sbjct: 311 GAKAAGNT-DPQAVAEAIKAKGPFKTAIGELGFDEKGDITRPDYVMYTWKKG 361 Lambda K H 0.312 0.131 0.362 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: 446 Number of extensions: 23 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: 367 Length of database: 372 Length adjustment: 30 Effective length of query: 337 Effective length of database: 342 Effective search space: 115254 Effective search space used: 115254 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 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