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_086508511.1 BZY95_RS02775 ABC transporter ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_002151265.1:WP_086508511.1 Length = 230 Score = 163 bits (413), Expect = 2e-45 Identities = 89/210 (42%), Positives = 131/210 (62%), Gaps = 3/210 (1%) Query: 11 LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70 +L + ++HA Y + IL GV+ V GELVT++G NGAG+ST K I ++ TG I Sbjct: 1 MLRIRDLHAFY-GESHILHGVDMEVRRGELVTLLGRNGAGRSTTLKAIMSMVGRRTGSIM 59 Query: 71 FKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAMF 130 G G+K+++I RLG+ Y P+ +F SL VEENL + +R+ + D+I+ MF Sbjct: 60 INGTETVGMKAHRIPRLGIGYCPEERGIFASLDVEENLLLPPTVRSGGMSI--DEIYEMF 117 Query: 131 PRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQIN 190 P L +RRR + LSGGE+QMLAM + L +L+LDE + L+P++V ++ E + ++ Sbjct: 118 PNLYERRRSQGTRLSGGEQQMLAMARILRTGARMLLLDEITEGLAPVIVQKLAEVLVKLR 177 Query: 191 QEGTAIILVEQNARKALEMADRGYVLESGR 220 G I+LVEQN R A +ADR YV+E GR Sbjct: 178 DRGMTIVLVEQNFRFAAPLADRHYVMEHGR 207 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: 134 Number of extensions: 4 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: 230 Length adjustment: 23 Effective length of query: 224 Effective length of database: 207 Effective search space: 46368 Effective search space used: 46368 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 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