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_067073807.1 MCUHO_RS04180 ATP-binding cassette domain-containing protein
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_001602375.1:WP_067073807.1 Length = 277 Score = 104 bits (260), Expect = 2e-27 Identities = 74/230 (32%), Positives = 118/230 (51%), Gaps = 5/230 (2%) Query: 11 LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70 LLE ++ Y +V L+GVNF E + VIGPNGAGKSTL K G+L P +G++ Sbjct: 3 LLETRSLTHIYRGNVHALEGVNFTAERKSRIAVIGPNGAGKSTLFKHFNGILKPTSGEVL 62 Query: 71 FKGKNIAGLKSNQIVR-LGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAM 129 KG+ I ++ + +G+ + +F S +VE+++ G + ++ Sbjct: 63 IKGEPITNANVREVRKFVGIVFQNPDDQIF-SPTVEQDVAFGPINLGLDETTVAHRVEEA 121 Query: 130 FPRL--SDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVK 187 L D R + LSGGE++ +A+ L +EP +LVLDEP+A L P VT + V Sbjct: 122 LHLLGIEDLRERVPHHLSGGEKKRVAIAGILAMEPEVLVLDEPTAGLDPQGVTDLVRFVN 181 Query: 188 QINQE-GTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKV 236 ++ +E G ++ + EMAD YV++ G SG E+ P++ Sbjct: 182 RLPEEYGMTVVFSTHHLDLVAEMADYVYVMDRGTIVGSGTVGEVFARPEL 231 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: 8 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: 277 Length adjustment: 25 Effective length of query: 222 Effective length of database: 252 Effective search space: 55944 Effective search space used: 55944 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