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 5210736 Shew_3164 ABC transporter-related protein (RefSeq)
Query= TCDB::Q8YT15 (247 letters) >FitnessBrowser__PV4:5210736 Length = 241 Score = 107 bits (268), Expect = 2e-28 Identities = 70/225 (31%), Positives = 126/225 (56%), Gaps = 15/225 (6%) Query: 11 LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70 ++++ N+H Y D +L+G++ + GE+V+VIGP+G+GKST + I L P G+I Sbjct: 1 MIKISNLHK-YFGDNQVLKGIDESIARGEVVSVIGPSGSGKSTFLRCINLLEQPTQGEIV 59 Query: 71 FKGKNIAGLKS---NQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKD-KI 126 G++I + ++GM + Q N+FP +V++N+ + Q D + Sbjct: 60 IDGQSITAPDACIDKLRQKVGMVF--QNFNLFPHKTVQQNITLAPVKLGLMTQAEADSEA 117 Query: 127 FAMFPR--LSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFE 184 + + LSD+ +LSGG++Q +A+ +AL ++P L++ DEP++AL P +V V + Sbjct: 118 MRLLDQVGLSDKASAYPASLSGGQKQRVAIARALAMKPELMLFDEPTSALDPEMVGDVLD 177 Query: 185 QVKQINQEGTAIILVEQNARKALEMADR------GYVLESGRDAI 223 +KQ+ Q G +++V A +++DR GYV+ES A+ Sbjct: 178 VMKQLAQAGMTMVIVTHEMGFAKDVSDRVIFMDGGYVVESNVPAL 222 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: 153 Number of extensions: 8 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: 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