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 Pf1N1B4_3974 ABC transporter, ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3974 Length = 341 Score = 111 bits (277), Expect = 2e-29 Identities = 68/213 (31%), Positives = 123/213 (57%), Gaps = 9/213 (4%) Query: 12 LEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITF 71 +++EN+ Y ++D + N VE GE V+++GP+G GK+T + I G + +G+I Sbjct: 4 VQLENLGKRY-GEIDAVVATNLSVEKGEFVSLLGPSGCGKTTTLQMIAGFVEVSSGRIVL 62 Query: 72 KGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIR---NDSLQPLKDKIFA 128 G++I K G+ V Q +FP ++V +N+ G +R ND LQ D++ Sbjct: 63 DGRDITHAKP---ASRGLGVVFQSYALFPHMTVRDNVAFGLRMRKVPNDELQQRVDRVLK 119 Query: 129 MFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQ 188 + RL+ + LSGG+RQ +A+ +AL++EP +L+LDEP + L L ++ ++++ Sbjct: 120 LV-RLNQHAERYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDANLREEMQFEIRR 178 Query: 189 INQE-GTAIILVEQNARKALEMADRGYVLESGR 220 I +E G ++V + +AL ++DR V+++GR Sbjct: 179 IQREVGITTLMVTHDQSEALSISDRVVVMQAGR 211 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: 202 Number of extensions: 10 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: 341 Length adjustment: 26 Effective length of query: 221 Effective length of database: 315 Effective search space: 69615 Effective search space used: 69615 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: 48 (23.1 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