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_011652366.1 RL_RS14680 ABC transporter ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_000009265.1:WP_011652366.1 Length = 241 Score = 196 bits (497), Expect = 5e-55 Identities = 102/237 (43%), Positives = 151/237 (63%), Gaps = 9/237 (3%) Query: 11 LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70 +LE+++V+ GY K + IL GV+F++ + T+IGPNGAGKST+ K IFGLL H+G++ Sbjct: 1 MLELKDVYGGYGK-ITILNGVSFKIPRASITTIIGPNGAGKSTVFKAIFGLLDIHSGQVL 59 Query: 71 FKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLK-----DK 125 G+++ G K ++ G+ YVPQ N+ P LSV NLE+G S P K D Sbjct: 60 LDGQDVTGCKPRDLIGRGVSYVPQGRNIVPQLSVYHNLELGGIT---SKNPSKVGERIDV 116 Query: 126 IFAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQ 185 + FP L R ++A LSGG+++ L + +AL+L+P L+++DEPS LSP LV +VF Sbjct: 117 VMEQFPALKTHRDRKAIELSGGQQKQLEVARALLLDPKLILIDEPSIGLSPNLVQEVFRT 176 Query: 186 VKQINQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLG 242 + ++ +G I++VEQNA+ AL M+D G VLE G+ + ELL DP+V L+LG Sbjct: 177 LIRLRDQGVTILMVEQNAKAALAMSDYGLVLELGQTRMHNKASELLADPRVGRLFLG 233 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: 188 Number of extensions: 14 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 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