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 GFF3116 HP15_3059 high-affinity branched-chain amino acid ABC transporter, ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >FitnessBrowser__Marino:GFF3116 Length = 233 Score = 213 bits (542), Expect = 3e-60 Identities = 106/233 (45%), Positives = 159/233 (68%), Gaps = 2/233 (0%) Query: 11 LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70 +L +E+VH Y K ++ L GV+ V+ GE+V++IG NGAGK+TL T+ G +G+I Sbjct: 1 MLVLEDVHTHYGK-IEALHGVSVEVKKGEIVSLIGANGAGKTTLLMTVCGNPRASSGRIF 59 Query: 71 FKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDS-LQPLKDKIFAM 129 +G+ I + QI+R G+ VP+ VF L+VEENL MG F + ++ ++ ++ + Sbjct: 60 LEGREITNESTAQIMRSGIAIVPEGRRVFSGLTVEENLHMGGFFNTKAEIRKSQEHVYEL 119 Query: 130 FPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQI 189 FPRL +R QRAGT+SGGE+QMLA+G+ALM P +++LDEPS L+P+++ Q+FE + Q+ Sbjct: 120 FPRLKEREHQRAGTMSGGEQQMLAIGRALMSRPEMIILDEPSLGLAPLIIKQIFEIIGQL 179 Query: 190 NQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLG 242 +EG + LVEQNA +AL +ADRGYVLE+G+ + G+ LL +P V YLG Sbjct: 180 REEGITVFLVEQNAHQALNLADRGYVLETGKIRLHDTGKNLLNNPDVQNAYLG 232 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: 3 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: 233 Length adjustment: 23 Effective length of query: 224 Effective length of database: 210 Effective search space: 47040 Effective search space used: 47040 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