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_110206122.1 DNK54_RS06395 ABC transporter ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_003194585.1:WP_110206122.1 Length = 262 Score = 186 bits (473), Expect = 3e-52 Identities = 101/243 (41%), Positives = 149/243 (61%), Gaps = 7/243 (2%) Query: 11 LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70 +L + N+ Y V +L GV+ VE G +V ++GPNGAGK+TLA+ + GLL H G +T Sbjct: 1 MLSIRNLEVAYQDVVHVLHGVSLEVERGAVVALLGPNGAGKTTLARAVSGLLPIHDGSVT 60 Query: 71 -----FKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRN--DSLQPLK 123 + +++ GL S +G+ V + +F S++VEENL G F ++ L+ Sbjct: 61 GGTIAWGDQSLLGLDSRARSAMGIAQVMEGRRIFTSMTVEENLVAGGFTKSARKHLRDRT 120 Query: 124 DKIFAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVF 183 + +AMFPRL++RR+QRAG LSGGE+QMLA+ +ALM P LL+LDEP+ L+P + + Sbjct: 121 EDAYAMFPRLAERRKQRAGYLSGGEQQMLAIARALMSGPELLILDEPTLGLAPSVRDYLR 180 Query: 184 EQVKQINQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLGA 243 + +N GT ++LVEQNA AL+++ Y+LE+GR G EL DP + E YLG Sbjct: 181 GVIADVNSRGTTVLLVEQNADLALDVSFYTYILEAGRVVHDGASSELREDPDIQEFYLGI 240 Query: 244 GKG 246 G Sbjct: 241 HDG 243 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: 6 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: 262 Length adjustment: 24 Effective length of query: 223 Effective length of database: 238 Effective search space: 53074 Effective search space used: 53074 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: 47 (22.7 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