Align NatC aka SLL0146, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_012045993.1 BBTA_RS28615 branched-chain amino acid ABC transporter permease
Query= TCDB::P74455 (372 letters) >NCBI__GCF_000015165.1:WP_012045993.1 Length = 332 Score = 89.0 bits (219), Expect = 2e-22 Identities = 46/126 (36%), Positives = 74/126 (58%), Gaps = 1/126 (0%) Query: 1 MNFG-YLIFLITSAATYGIFALGLNLQWGFAGLINFGHVAFMTLGAYATTLLSLRGLPIP 59 MNF Y +++++ A I A+GLNL G+AG ++ AF+ +GAY +L+ G P+ Sbjct: 25 MNFNRYGLYILSQWAVMTIAAMGLNLTLGYAGQVSLAQGAFVGIGAYGAAILTTHGWPLI 84 Query: 60 LAVLVGMGLAMALGLLIGTSTLRLREDYLAIVTIGVSELIRLIANNEEWLTQGTFGVQSF 119 A+ + + + +G L+G LR++ YLA VT+ S L+ L+ NE WLT G +G+ + Sbjct: 85 SALGLVIVICFIVGWLLGYPALRVQHHYLAFVTLAFSTLMFLVFRNESWLTNGIYGISNI 144 Query: 120 PWPMDF 125 P P F Sbjct: 145 PRPEIF 150 Score = 70.9 bits (172), Expect = 5e-17 Identities = 46/153 (30%), Positives = 74/153 (48%), Gaps = 12/153 (7%) Query: 211 LALTLLALTYAGLEFWVHSPWGRILKAIREDEEIPRALGKNVFWYKLQAFMGGGAIAGLA 270 L L L L + + + SPWGR A+RE+ ++LG + Y L AF G A+ G+A Sbjct: 163 LCLGSLGLVTLAMWWLIRSPWGRAFMALRENPIRAQSLGIDTRRYTLMAFAIGSALGGIA 222 Query: 271 GALFAWQLTSIYPSNFDTLLTFNAWIIVVLGGAGSNAGTVLGTIIFWAYDSLTRFLLPQI 330 G L+A + P F+ L+ + ++V++GG+G G LG +I RF Sbjct: 223 GVLYAPLTQYVDPVPFNLQLSLDLLMMVIVGGSGFMLGPFLGAMIAVLLPEWLRF----- 277 Query: 331 AFLDQSQAGALRVMVIGLILMVLMVWRPQGILG 363 A +M+ ++ L+++ P GILG Sbjct: 278 -------AEGYYLMLYAAAVIALLIYSPSGILG 303 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: 377 Number of extensions: 21 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 372 Length of database: 332 Length adjustment: 29 Effective length of query: 343 Effective length of database: 303 Effective search space: 103929 Effective search space used: 103929 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: 49 (23.5 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