Align NatE, 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_0841 Dsui_0841 ABC-type branched-chain amino acid transport systems, ATPase component
Query= TCDB::Q8YT15 (247 letters) >FitnessBrowser__PS:Dsui_0841 Length = 251 Score = 221 bits (564), Expect = 8e-63 Identities = 119/241 (49%), Positives = 167/241 (69%), Gaps = 9/241 (3%) Query: 10 PLLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKI 69 P+LEV ++ Y K V+ L V+ R+ GE+VTVIGPNGAGK+TL + GLL P+ G++ Sbjct: 9 PVLEVSDLCVAYGK-VEALHKVSLRIREGEIVTVIGPNGAGKTTLLSALMGLL-PYRGEV 66 Query: 70 TFKGKNI-AGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIR-----NDSLQPLK 123 + N+ A ++ + V G+ VP+ +F +SVE+NL +GAF R D Q ++ Sbjct: 67 AYVSHNLDAHVEVEERVGQGLTLVPEKRELFAEMSVEDNLLLGAFHRYRSGLRDHAQTME 126 Query: 124 DKIFAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVF 183 + +FA+FPRL +RR Q AGTLSGGERQMLAMG+ALM +P LL+LDEPS L+P+++ ++F Sbjct: 127 E-VFALFPRLKERRTQAAGTLSGGERQMLAMGRALMAKPKLLMLDEPSLGLAPLIIKEIF 185 Query: 184 EQVKQINQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLGA 243 V ++ Q G +I+LVEQNAR AL++AD GYVLE+G ++ GP EL DP+V E YLG Sbjct: 186 RIVAELKQTGVSILLVEQNARAALQVADYGYVLETGEVSLEGPSHELADDPRVIETYLGL 245 Query: 244 G 244 G Sbjct: 246 G 246 Lambda K H 0.317 0.136 0.377 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: 184 Number of extensions: 9 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: 247 Length of database: 251 Length adjustment: 24 Effective length of query: 223 Effective length of database: 227 Effective search space: 50621 Effective search space used: 50621 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 46 (22.3 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