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 PfGW456L13_876 Glutamate transport ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_876 Length = 245 Score = 111 bits (277), Expect = 2e-29 Identities = 75/241 (31%), Positives = 131/241 (54%), Gaps = 19/241 (7%) Query: 10 PLLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKI 69 PLL + +H Y D +L+G++ +E G++V +IG +G+GKSTL +T+ GL + + G I Sbjct: 2 PLLRISALHK-YYGDHHVLKGIDLSIEEGQVVAIIGRSGSGKSTLLRTLNGLESINDGVI 60 Query: 70 TFKGKNIAGLKSN-QIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFA 128 G+ + +++ + +R + V Q N+FP L+V EN+ + Q ++ A Sbjct: 61 EVDGEYLDAARADLRSLRQKVGMVFQQFNLFPHLTVGENVMLAP-------QVVQKVPKA 113 Query: 129 MFPRLSDRRRQRAGT----------LSGGERQMLAMGKALMLEPSLLVLDEPSAALSPIL 178 L+ + +R G LSGG++Q +A+ +AL + P +L+ DE ++AL P L Sbjct: 114 KAAELARQMLERVGLGEKFDAFPDRLSGGQQQRVAIARALAMSPKVLLCDEITSALDPEL 173 Query: 179 VTQVFEQVKQINQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAE 238 V +V V+Q+ +EG +I+V R A E+ D+ + G+ G + L +P+ AE Sbjct: 174 VNEVLSVVRQLAREGMTLIMVTHEMRFAREVGDKLVFMHQGKVHEVGDPKVLFANPQTAE 233 Query: 239 L 239 L Sbjct: 234 L 234 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: 153 Number of extensions: 9 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: 247 Length of database: 245 Length adjustment: 24 Effective length of query: 223 Effective length of database: 221 Effective search space: 49283 Effective search space used: 49283 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