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 GFF3113 HP15_3056 high-affinity branched-chain amino acid ABC transporter, permease protein
Query= TCDB::Q8YXD0 (288 letters) >FitnessBrowser__Marino:GFF3113 Length = 307 Score = 150 bits (380), Expect = 3e-41 Identities = 89/292 (30%), Positives = 160/292 (54%), Gaps = 17/292 (5%) Query: 7 QLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNT----FGVNIW 62 Q ++NG+ +GS AL A+G T+ YGI+ + NFAHG+ +GAY T G+ W Sbjct: 9 QQLINGLTIGSTYALIAIGYTMVYGIIGMINFAHGEIYMIGAYTALIAITGLAALGI-AW 67 Query: 63 LSMIVAVVGTVGVMLLSEKLLWS----RMRSIRANSTTLIIIS-IGLALFLRNGIILIWG 117 L +I+ +V + M++S + W+ R +R + +IS IG+++FL+N + L G Sbjct: 68 LPLIL-IVALLCAMIVSSSMGWAVERVAYRPVRGRHRLIPLISAIGMSIFLQNYVHLAQG 126 Query: 118 GRNQNYNLPITPAL-----DIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAV 172 RN + I D F + + Q+ + ++ + AL + ++ G+A RAV Sbjct: 127 SRNIGFPALIDGGFNFGSGDGFQMSLSYMQITIFITTLICMTALSLFISRSRTGRACRAV 186 Query: 173 ADDLDLAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGLIT-AVRPNMGWFLILPLFASVI 231 + DL +A + GID ++I T++I + ++ G + G+ +V P G+ L F + + Sbjct: 187 SQDLGMANLLGIDTNRIISATFVIGAALAAVAGLLLGMYYGSVDPLFGFIAGLKAFTAAV 246 Query: 232 LGGIGNPYGAIAAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGL 283 LGGIG+ GA+ I+G+ + +++ +L +YK ++ ++IL+LL +P GL Sbjct: 247 LGGIGSIPGAMLGGLILGVAESMTSGYLSGEYKDVISFSLLILILLFKPTGL 298 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: 4 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: 307 Length adjustment: 26 Effective length of query: 262 Effective length of database: 281 Effective search space: 73622 Effective search space used: 73622 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