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_110205943.1 DNK54_RS05355 ABC transporter ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_003194585.1:WP_110205943.1 Length = 321 Score = 122 bits (305), Expect = 1e-32 Identities = 75/240 (31%), Positives = 122/240 (50%), Gaps = 19/240 (7%) Query: 20 GYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITFKGKNIAGL 79 G +K VD+ + V+ G + +IGPNGAGK+T + G P G +F G + + Sbjct: 55 GGLKAVDV---AHLEVQRGVITALIGPNGAGKTTFFNLLTGFDRPDDGTWSFNGTKLNRM 111 Query: 80 KSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDS------LQPL--------KDK 125 + ++ RLGM Q+ V L+V EN+ + A + PL D+ Sbjct: 112 PAYRVARLGMVRTFQLTKVLSRLTVLENMRVAARGQTGERWWAALFAPLWRGQENENTDR 171 Query: 126 IFAMFPR--LSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVF 183 + R L + AG+LSGG+R++L M +ALM++P L++LDEP A ++P L + Sbjct: 172 AHDLLARFLLDKKAADFAGSLSGGQRKLLEMARALMVDPELVMLDEPMAGVNPALKQSLL 231 Query: 184 EQVKQINQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLGA 243 VK + EG ++ VE + +++D V+ G+ GP ++ DP+V + YLGA Sbjct: 232 GHVKSLRDEGRTVLFVEHDMDMVRDISDWVVVMAQGQVIAEGPPDSVMADPRVIDAYLGA 291 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: 166 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: 321 Length adjustment: 26 Effective length of query: 221 Effective length of database: 295 Effective search space: 65195 Effective search space used: 65195 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