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_011384838.1 AMB_RS12350 ABC transporter ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_000009985.1:WP_011384838.1 Length = 234 Score = 191 bits (485), Expect = 1e-53 Identities = 101/235 (42%), Positives = 153/235 (65%), Gaps = 5/235 (2%) Query: 11 LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70 +L+V ++ Y D L GV+F V G + ++G NGAGK++L + I G+ P G I Sbjct: 1 MLDVRDLDLFY-GDAQALAGVSFTVPDGSITAIVGANGAGKTSLIRAIAGMEPPRAGSIR 59 Query: 71 FKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFI---RNDSLQPLKDKIF 127 F G +I G +S +I LG+ V + VFP++SV++NLE+GA + R + Q L ++++ Sbjct: 60 FDGHDITGKESFEICDLGLGQVAEGRQVFPTMSVQDNLELGAMVPRARKLATQSL-ERVW 118 Query: 128 AMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVK 187 MFPRL +RR+Q AGTLSGGE+QMLA+G+ LM P +++ DEPS LSP +V +VF ++ Sbjct: 119 EMFPRLLERRKQLAGTLSGGEQQMLAIGRCLMGRPKMIMFDEPSLGLSPAMVHEVFAIIR 178 Query: 188 QINQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLG 242 +++++G ++LVEQN +L MAD VLE+G + G G +LL D +V YLG Sbjct: 179 RLHEDGMTVVLVEQNVAVSLHMADHACVLENGHVVMEGRGADLLGDDRVRAAYLG 233 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: 171 Number of extensions: 5 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: 234 Length adjustment: 23 Effective length of query: 224 Effective length of database: 211 Effective search space: 47264 Effective search space used: 47264 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