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 Synpcc7942_2177 Synpcc7942_2177 integral membrane protein of the ABC-type Nat permease for neutral amino acids NatD
Query= TCDB::Q8YXD0 (288 letters) >FitnessBrowser__SynE:Synpcc7942_2177 Length = 296 Score = 334 bits (856), Expect = 2e-96 Identities = 163/281 (58%), Positives = 215/281 (76%) Query: 4 QTIQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNTFGVNIWL 63 Q QL +NG+A GS++ALAA GLTL YGILRL+NFA G+FLTLGAY T N+ G+++WL Sbjct: 14 QLAQLAINGLATGSLLALAATGLTLIYGILRLTNFAQGEFLTLGAYFTLVANSLGLSLWL 73 Query: 64 SMIVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWGGRNQNY 123 ++ + + T+ + LL E +LW +R R N+TTLII++IGL+LFLRN +ILIWG NQ Y Sbjct: 74 AIPLGAIATIALCLLGEAVLWEPLRRQRVNTTTLIILTIGLSLFLRNLVILIWGAGNQAY 133 Query: 124 NLPITPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDLDLAKVSG 183 L + PAL ++G+++ N LLV+ A ++ LH++LQ T IGK MRA+ADD DLA+VSG Sbjct: 134 RLAVQPALTLWGLRITLNSLLVVIGAAAALVLLHWVLQRTSIGKGMRAIADDPDLARVSG 193 Query: 184 IDVEQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLILPLFASVILGGIGNPYGAIA 243 + VE VI WTW+IAG +T++ G +YGLITAVRP MGW LILPLFAS ILGGIG+PYGAIA Sbjct: 194 VPVETVIRWTWVIAGGLTAIAGGLYGLITAVRPTMGWNLILPLFASAILGGIGSPYGAIA 253 Query: 244 AAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGLF 284 I+G QE+ST +L ++YK VA +I+I VL+IRP+GLF Sbjct: 254 GGLILGFAQELSTYWLPAEYKLAVAFVILIGVLVIRPQGLF 294 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: 295 Number of extensions: 9 Number of successful extensions: 1 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: 296 Length adjustment: 26 Effective length of query: 262 Effective length of database: 270 Effective search space: 70740 Effective search space used: 70740 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