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 WP_069956504.1 BEN30_RS01130 urea ABC transporter ATP-binding subunit UrtE
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_001746755.1:WP_069956504.1 Length = 231 Score = 136 bits (342), Expect = 4e-37 Identities = 74/220 (33%), Positives = 127/220 (57%), Gaps = 8/220 (3%) Query: 22 IKDVDI-------LQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITFKGK 74 ++D+D+ L+GV+ +G++ V+G NG GK++L + I G GK+ ++ Sbjct: 4 VQDIDLHYGASQALRGVDLSAATGQVTCVMGRNGVGKTSLMRAIVGQQGTSAGKVMWEDD 63 Query: 75 NIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAMFPRLS 134 +I L ++ R G+ +VPQ +FP +SVEENL G SL+ ++D+IF +FP L Sbjct: 64 DITKLSPHERARRGIAFVPQGREIFPLMSVEENLRTGFAAVPRSLRHVQDEIFDLFPVLK 123 Query: 135 DRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQINQEG- 193 D +R G LSGG++Q LA+ +AL+ P LLVLDEP+ + P ++ + ++ + G Sbjct: 124 DMLHRRGGDLSGGQQQQLAIARALVTRPRLLVLDEPTEGIQPSIIKDIERVIRLLASRGD 183 Query: 194 TAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTD 233 ++LVEQ A ++AD V++ G ++G E++ + Sbjct: 184 MGVLLVEQYFEFARDLADTFCVMDRGEVVLAGTKAEMVEE 223 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: 149 Number of extensions: 10 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: 231 Length adjustment: 23 Effective length of query: 224 Effective length of database: 208 Effective search space: 46592 Effective search space used: 46592 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 24 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