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 AO356_28995 AO356_28995 ABC transporter ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28995 Length = 258 Score = 178 bits (452), Expect = 8e-50 Identities = 99/241 (41%), Positives = 150/241 (62%), Gaps = 9/241 (3%) Query: 11 LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHT---- 66 LL V+++ Y + + GV+ RV G++V ++G NGAGKST K I GL+ Sbjct: 14 LLAVQDIEVIYDGAILAVAGVSLRVGQGDIVALLGANGAGKSTTLKAISGLVQADRAQVS 73 Query: 67 -GKITFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLK-- 123 G+I F+G++ AG+ +N + R G+ +V + +VF L++E+NL G F+R + + L+ Sbjct: 74 RGRIVFQGQDTAGVAANLLARRGIVHVLEGRHVFAHLTIEDNLRSGGFLRKPTRRELEHD 133 Query: 124 -DKIFAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQV 182 ++I+A FPRL +R+ +AG SGGE+QMLA+G+ALM +P L++LDEPS L+PILV ++ Sbjct: 134 LERIYAWFPRLKTKRKTQAGLTSGGEQQMLAIGRALMTQPRLVLLDEPSMGLAPILVEEI 193 Query: 183 FEQVKQIN-QEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYL 241 F V Q+N QEG + ++ EQN AL A Y+LE+GR G EL + YL Sbjct: 194 FAIVAQLNAQEGVSFLVAEQNINVALRHASYAYILENGRVVGEGDATELAAREDLQHFYL 253 Query: 242 G 242 G Sbjct: 254 G 254 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: 173 Number of extensions: 9 Number of successful extensions: 4 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: 258 Length adjustment: 24 Effective length of query: 223 Effective length of database: 234 Effective search space: 52182 Effective search space used: 52182 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