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 WP_084005217.1 BEN30_RS07660 ABC transporter ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_001746755.1:WP_084005217.1 Length = 262 Score = 146 bits (368), Expect = 5e-40 Identities = 84/226 (37%), Positives = 136/226 (60%), Gaps = 10/226 (4%) Query: 21 YIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHT--GKITFKGKNIAG 78 Y + I+QGVNF + GE+V ++G NGAGK++ +TI + P G+I + + Sbjct: 40 YYGESYIVQGVNFDIHEGEIVALLGRNGAGKTSTLRTIARMDDPQLRHGEIWLDHQPLHT 99 Query: 79 LKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLK---DKIFAMFPRLSD 135 ++S Q RLG+ VP+ ++ P L+VEENL + P+ ++I+ FPRL++ Sbjct: 100 MQSWQAARLGVGLVPEDRSIIPGLTVEENLTLSQIA-----PPIGWSIERIYEHFPRLAE 154 Query: 136 RRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQINQEGTA 195 RR Q TLSGGE+QMLA+ +AL + LL+LDEP L+P++V ++ ++ + + G Sbjct: 155 RRMQEGVTLSGGEQQMLAVARALARDIKLLLLDEPYEGLAPVIVHEIESILEGVKKLGIT 214 Query: 196 IILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYL 241 I+VEQNA AL ++DR +L+ G +G QE+L + ++ + YL Sbjct: 215 TIIVEQNAIAALHLSDRAIILDMGEVVFNGSAQEVLDNKELRDEYL 260 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: 155 Number of extensions: 7 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: 262 Length adjustment: 24 Effective length of query: 223 Effective length of database: 238 Effective search space: 53074 Effective search space used: 53074 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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