Align NatC aka SLL0146, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_041938756.1 FRAAL_RS03130 branched-chain amino acid ABC transporter permease
Query= TCDB::P74455 (372 letters) >NCBI__GCF_000058485.1:WP_041938756.1 Length = 515 Score = 88.2 bits (217), Expect = 5e-22 Identities = 49/121 (40%), Positives = 70/121 (57%), Gaps = 9/121 (7%) Query: 9 LITSAATYGIFALGLNLQWGFAGLINFGHVAFMTLGAYATTLL-SLRGLPI-------PL 60 ++ Y + ALGLN+ G+AGL++ G++AF +GAYAT S +P P Sbjct: 201 MVNDIGIYALLALGLNVVVGYAGLLDLGYIAFFAIGAYATAYFTSQTAMPWHAPFVLNPF 260 Query: 61 AVL-VGMGLAMALGLLIGTSTLRLREDYLAIVTIGVSELIRLIANNEEWLTQGTFGVQSF 119 V + + LA G+++G TLRLR DYLAIVT+G E+I L+ANN + +T G G Sbjct: 261 FVFPIALVLAALAGVILGAPTLRLRGDYLAIVTLGFGEIIHLVANNADGITNGARGAFGV 320 Query: 120 P 120 P Sbjct: 321 P 321 Score = 67.4 bits (163), Expect = 8e-16 Identities = 48/155 (30%), Positives = 77/155 (49%), Gaps = 15/155 (9%) Query: 209 MLLALTL-LALTYAGLEFWVHSPWGRILKAIREDEEIPRALGKNVFWYKLQAFMGGGAIA 267 +LLA+ + + + + LE S GR AIREDE A G KL AF G +++ Sbjct: 344 LLLAIVIGVMIAFGRLE---RSRIGRSWAAIREDEIAAEATGVATLRMKLLAFAIGASVS 400 Query: 268 GLAGALFAWQLTSIYPSNFDTLLTFNAWIIVVLGGAGSNAGTVLGTIIFWAYDSLTRFLL 327 G AG LFA P +F +F +V+ GG GS G V+G ++ L +L Sbjct: 401 GFAGVLFA-SKQFFNPQSFSLQASFFVVAVVIFGGMGSRLGVVVGAVVL---QGLAFYLR 456 Query: 328 PQIAFLDQSQAGALRVMVIGLILMVLMVWRPQGIL 362 ++ D R + G +++++M++RPQG++ Sbjct: 457 DKVQPAD-------RYIYFGAVIVIMMIFRPQGLV 484 Score = 25.4 bits (54), Expect = 0.004 Identities = 38/137 (27%), Positives = 58/137 (42%), Gaps = 17/137 (12%) Query: 1 MNFGYLIFLITSAATYGIFALGLNLQWGFAGLINFGHVAFMTLGA-YATTLLSLRGLPIP 59 + FG +I L+ + A + G G H++ LG Y + L + Sbjct: 294 LGFGEIIHLVANNAD--------GITNGARGAFGVPHLSIDLLGIDYKWGIDPLPYYYLL 345 Query: 60 LAVLVGMGLAMALGLL----IGTSTLRLREDYLAIVTIGVSEL-IRLIANNEEWLTQGTF 114 LA+++G+ +A G L IG S +RED +A GV+ L ++L+A G Sbjct: 346 LAIVIGV--MIAFGRLERSRIGRSWAAIREDEIAAEATGVATLRMKLLAFAIGASVSGFA 403 Query: 115 GVQSFPWPMDFNPTLLS 131 GV F FNP S Sbjct: 404 GV-LFASKQFFNPQSFS 419 Lambda K H 0.327 0.143 0.442 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: 406 Number of extensions: 19 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 372 Length of database: 515 Length adjustment: 32 Effective length of query: 340 Effective length of database: 483 Effective search space: 164220 Effective search space used: 164220 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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