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 Dsui_2060 Dsui_2060 branched-chain amino acid ABC-type transport system, permease component
Query= TCDB::Q8YXD0 (288 letters) >FitnessBrowser__PS:Dsui_2060 Length = 293 Score = 139 bits (351), Expect = 6e-38 Identities = 87/284 (30%), Positives = 156/284 (54%), Gaps = 8/284 (2%) Query: 7 QLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTF-FVNTFGVNIWLSM 65 Q ++N + +GS+ AL A+G TL +G+L + N +HG +G+Y V+ +W++M Sbjct: 4 QQLLNALTLGSVYALFALGFTLVFGVLAVINLSHGAVFMVGSYAALAMVSHLNAPLWVAM 63 Query: 66 IVAVV--GTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWGGRNQNY 123 + A+V GT+G LL + L+ +R+ A +I +IG+ + L + ++G + Sbjct: 64 LGAMVVSGTIG--LLVDVLVLKPLRARNAPHLIPMIATIGVGIMLTSAAQGLFGAEVLRF 121 Query: 124 NLPITPALDIF--GVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDLDLAKV 181 + PA + V V ++ ++A+A L + L +L+ T++G+A+RA+A+ A + Sbjct: 122 PEDVMPAGEFMVGDVHVRALEIAIVAIAFLLMAVLFTILKRTQLGRALRAIAESPKAAYL 181 Query: 182 SGIDVEQVIFWTWLIAGTVTSLGGSMYGL-ITAVRPNMGWFLILPLFASVILGGIGNPYG 240 GI+VE + T +A + + G + GL A+ P MG ++ A +ILGG+G+ G Sbjct: 182 LGINVEGLFHITSFVAAALGGIAGVLIGLNFNAITPFMGQPMLHKGIAVIILGGMGDIRG 241 Query: 241 AIAAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGLF 284 A+ +G + +S +L SQ VA ++ L+LL+RP GLF Sbjct: 242 ALIGGLFLGFAEVISKAYLSSQMGDAVAFGLLFLILLVRPSGLF 285 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: 230 Number of extensions: 10 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: 293 Length adjustment: 26 Effective length of query: 262 Effective length of database: 267 Effective search space: 69954 Effective search space used: 69954 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