Align NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate WP_043743902.1 AMB_RS08455 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8YXD0 (288 letters) >NCBI__GCF_000009985.1:WP_043743902.1 Length = 291 Score = 143 bits (360), Expect = 5e-39 Identities = 87/283 (30%), Positives = 154/283 (54%), Gaps = 9/283 (3%) Query: 6 IQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNTFGVNIWLSM 65 +Q + +G+ G+I ALA +G + Y + NFA G+F+ +G T + GV I+L++ Sbjct: 6 LQYLFSGLTSGAIYALAGLGFAIIYNASHVINFAQGEFIMIGGMATATMVAAGVPIYLAI 65 Query: 66 IVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWGGRNQNYNL 125 +A+ ++ V + EK R+ A+ T+III+IG ++F+R LIW + ++L Sbjct: 66 PLAMAASMLVGVAMEKFAIEPARN--ADVVTIIIITIGASIFMRGAAQLIWD--KEFHSL 121 Query: 126 PI----TPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDLDLAKV 181 P TP + + G + L V ++ ++I L Y T GKAM + + A++ Sbjct: 122 PAFSGETP-IAVMGATLMPQSLWVFGISAVAIALLWYFFNRTMFGKAMLGTSHNRLAAQL 180 Query: 182 SGIDVEQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLILPLFASVILGGIGNPYGA 241 G+ V++V+ ++ ++ + ++GG + IT G L L F++ +LGG+GN GA Sbjct: 181 VGVAVKRVLLASFALSALLGAVGGIVVTPITFTNYEAGIMLGLKGFSAAVLGGLGNGTGA 240 Query: 242 IAAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGLF 284 I I+GI + +++ +L S YK +A +I++ VL P GLF Sbjct: 241 IIGGLIVGIAEAMASGYLSSAYKDAIAFIIILFVLFFMPSGLF 283 Lambda K H 0.328 0.144 0.426 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: 222 Number of extensions: 12 Number of successful extensions: 3 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: 288 Length of database: 291 Length adjustment: 26 Effective length of query: 262 Effective length of database: 265 Effective search space: 69430 Effective search space used: 69430 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: 48 (23.1 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