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 SMc01948 SMc01948 high-affinity branched-chain amino acid ABC transporter ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >FitnessBrowser__Smeli:SMc01948 Length = 241 Score = 210 bits (535), Expect = 2e-59 Identities = 113/240 (47%), Positives = 163/240 (67%), Gaps = 7/240 (2%) Query: 10 PLLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKI 69 PLL V +V Y ++ L GV+ V GE+V +IG NGAGKSTL TI G TG + Sbjct: 4 PLLHVRSVET-YYGNIRALNGVDMEVHRGEIVALIGANGAGKSTLMMTICGSPQARTGSV 62 Query: 70 TFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKD---KI 126 F G++I L +++I RL + P+ +FP ++V ENL+MGA + D+L+ K+ K+ Sbjct: 63 HFDGQDITRLPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGASL--DNLKHFKEDVEKV 120 Query: 127 FAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQV 186 F +FPRL +R+ QR GTLSGGE+QML++G+ALM P LL+LDEPS L+P++V +FE + Sbjct: 121 FTLFPRLKERQAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAI 180 Query: 187 KQINQ-EGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLGAGK 245 K +N+ EG + LVEQNA AL+++DRGYV+ +GR +SG G++LL +P+V YL G+ Sbjct: 181 KVLNKNEGLTVFLVEQNAFGALKLSDRGYVMVNGRVTMSGSGKDLLANPEVRAAYLEGGR 240 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: 185 Number of extensions: 8 Number of successful extensions: 3 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: 241 Length adjustment: 24 Effective length of query: 223 Effective length of database: 217 Effective search space: 48391 Effective search space used: 48391 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