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 GFF4159 HP15_4099 branched-chain amino acid ABC transporter, ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >FitnessBrowser__Marino:GFF4159 Length = 269 Score = 208 bits (529), Expect = 1e-58 Identities = 110/243 (45%), Positives = 162/243 (66%), Gaps = 9/243 (3%) Query: 11 LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70 LLE++N+ Y K V +L+G++ RV G +V ++G NGAGKST K++ GLLT G++T Sbjct: 4 LLEIDNIEVVYNKSVQVLRGLSLRVPKGAIVALLGSNGAGKSTTLKSVSGLLTLEDGEVT 63 Query: 71 -----FKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDK 125 F+GK++ G+ ++VR G+ +V + VF L+VEENL + + S L D Sbjct: 64 AGEVRFRGKDVKGVPPERLVRDGLFHVMEGRRVFEDLTVEENLIAATYALSGSKPSLSDS 123 Query: 126 ---IFAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQV 182 ++ FPRL +RR+Q AG LSGGE+QMLA+G+AL+ +P L++LDEPS L+P+LV ++ Sbjct: 124 YELVYNYFPRLKERRKQLAGYLSGGEQQMLALGRALIAQPDLIMLDEPSLGLAPLLVEEI 183 Query: 183 FEQVKQINQE-GTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYL 241 F V +IN+E GTAI+LVEQNA +L +A GY++E+G+ I GP +L + V E YL Sbjct: 184 FTIVARINREQGTAILLVEQNAAVSLAIASYGYIMENGKIVIDGPADKLTANEDVQEFYL 243 Query: 242 GAG 244 G G Sbjct: 244 GVG 246 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: 215 Number of extensions: 6 Number of successful extensions: 4 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: 269 Length adjustment: 24 Effective length of query: 223 Effective length of database: 245 Effective search space: 54635 Effective search space used: 54635 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 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