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 GFF948 HP15_927 branched-chain amino acid ABC transporter, ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >FitnessBrowser__Marino:GFF948 Length = 240 Score = 152 bits (383), Expect = 8e-42 Identities = 88/231 (38%), Positives = 132/231 (57%), Gaps = 3/231 (1%) Query: 12 LEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITF 71 L + +HA Y + IL G++ V GELVT++G NGAG+ST K I ++ TG I Sbjct: 12 LRLSGLHAFY-GESHILHGIDMVVNRGELVTLLGRNGAGRSTTLKAIMNMVGRRTGSIMI 70 Query: 72 KGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAMFP 131 G+ + I RLG+ Y P+ +F SLSV+ENL + +R+ + ++I+ MFP Sbjct: 71 NGEETMSCAPHHIARLGVGYCPEHRGIFSSLSVQENLTLPPVVRSGGMS--LEEIYNMFP 128 Query: 132 RLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQINQ 191 L +RR + LSGGE+QMLAM + L ++L+LDE + L+P++V ++ E + + Sbjct: 129 NLYERRFSQGTKLSGGEQQMLAMARILRTGANMLLLDEITEGLAPVIVEKLGEVLIALKN 188 Query: 192 EGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLG 242 +G I+LVEQN A +ADR YV+E G+ EL V + YLG Sbjct: 189 KGLTIVLVEQNFHFAAPLADRHYVVEHGQIVEEVSANELSAKQSVLDGYLG 239 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: 150 Number of extensions: 6 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: 240 Length adjustment: 23 Effective length of query: 224 Effective length of database: 217 Effective search space: 48608 Effective search space used: 48608 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