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 AZOBR_RS29670 AZOBR_RS29670 ABC transporter permease
Query= TCDB::Q8YXD0 (288 letters) >FitnessBrowser__azobra:AZOBR_RS29670 Length = 290 Score = 171 bits (432), Expect = 2e-47 Identities = 95/281 (33%), Positives = 159/281 (56%), Gaps = 4/281 (1%) Query: 6 IQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFV-NTFGVNIWLS 64 +Q ++N + +G AL +GLTL +GI+R+ NF HG+ T GAY+ + + G+N ++S Sbjct: 5 LQHLLNAVVLGGTYALLGIGLTLIFGIMRVVNFTHGELYTFGAYMAYMLAGMMGLNFFMS 64 Query: 65 MIVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWGGRNQNYN 124 + +A V + + L E L ++ ++T L++I G+A+ + G L+WGG ++ Sbjct: 65 LAMAAVLGMALGALIEFTLLRPLKGADIDTTMLVMIGAGIAM--QAGEQLVWGGVAKSVP 122 Query: 125 LPITPALDIFG-VKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDLDLAKVSG 183 P + G V V N+L VL +A+L +G + L+ TK+G AMRA D D A + G Sbjct: 123 SPFPTEPVVLGSVSVGMNRLFVLGVALLLLGGFYLLINRTKLGVAMRATFQDPDTAALMG 182 Query: 184 IDVEQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLILPLFASVILGGIGNPYGAIA 243 ++ + T+ + + + G++ G I V P MG + L FA VILGG+GN GA Sbjct: 183 VNRGLMYTLTFALGSGLAATAGALLGPIFVVTPTMGDLVALKAFAIVILGGLGNIPGATI 242 Query: 244 AAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGLF 284 F++ + +E +L S Y+ + L++I VL++RP+GLF Sbjct: 243 GGFVLALAEEFGAGYLSSGYRDAMGFLLIIAVLIVRPQGLF 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: 245 Number of extensions: 19 Number of successful extensions: 2 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: 290 Length adjustment: 26 Effective length of query: 262 Effective length of database: 264 Effective search space: 69168 Effective search space used: 69168 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