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 RR42_RS34785 RR42_RS34785 ABC transporter permease
Query= TCDB::Q8YXD0 (288 letters) >FitnessBrowser__Cup4G11:RR42_RS34785 Length = 287 Score = 178 bits (452), Expect = 1e-49 Identities = 95/282 (33%), Positives = 162/282 (57%), Gaps = 3/282 (1%) Query: 6 IQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNT-FGVNIWLS 64 +Q ++NG+ +G + +L A+GLTL YGIL + NFAHG F GAY+++++ T G+N WL+ Sbjct: 5 LQQVLNGLTLGGVYSLVALGLTLVYGILHVPNFAHGAFYMAGAYVSYYLMTSLGMNYWLA 64 Query: 65 MIVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWGGRNQNYN 124 M A + + +L+++L++ +R+ A +I +IG+ LFL G +WG Sbjct: 65 MGAAAIAVAVLSMLADRLVFHPLRN--APELHDMIAAIGIMLFLEAGAQAMWGADFHRMP 122 Query: 125 LPITPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDLDLAKVSGI 184 P +++ G+ P +LL++A A + LH L T G + A+A + + A + GI Sbjct: 123 TPYGQMVEVMGLSAPAQRLLIIAAAFGLMVLLHLFLTRTVTGSTIVAMAQNREGAALVGI 182 Query: 185 DVEQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLILPLFASVILGGIGNPYGAIAA 244 D +V + I+G + ++ ++Y I V P+MG +I F +ILGG+G+ GAI Sbjct: 183 DATRVTLLVFAISGALAAIAATLYAPINLVYPSMGNLVITKAFVIIILGGMGSIPGAIVG 242 Query: 245 AFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGLFKG 286 IIG+ + ++ + YK +A +++L+L IRP+GLF G Sbjct: 243 GLIIGMAESFGGFYVSTDYKDIIAFALLVLILSIRPQGLFAG 284 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: 250 Number of extensions: 17 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: 287 Length adjustment: 26 Effective length of query: 262 Effective length of database: 261 Effective search space: 68382 Effective search space used: 68382 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: 47 (22.7 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