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_015797970.1 AFER_RS02585 ABC transporter ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_000023265.1:WP_015797970.1 Length = 254 Score = 198 bits (504), Expect = 8e-56 Identities = 106/236 (44%), Positives = 149/236 (63%), Gaps = 2/236 (0%) Query: 11 LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70 +L VE + AGY K I+ G++F ++VT+IGPNGAGKST K FGL+ GK+ Sbjct: 3 VLRVEGLTAGYGK-APIVDGISFHASVSQVVTLIGPNGAGKSTALKATFGLIPRMAGKVY 61 Query: 71 FKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAMF 130 +I L ++ R GM YVPQ+ NVF S+SVEENLE+G F+ SL K+ +F +F Sbjct: 62 LDETDITDLSAHHAARAGMAYVPQVDNVFASMSVEENLELGGFVERGSLDARKELVFEIF 121 Query: 131 PRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQIN 190 P L+ R+++AG LSGG+R ML MG+ALM P +++LDEP+A LSP V V+ Q+ Q+ Sbjct: 122 PALALARKRKAGLLSGGQRNMLGMGRALMSNPKVVLLDEPTAGLSPANVDVVWSQIAQVA 181 Query: 191 QEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLGAGKG 246 GT +++VEQN +AL AD Y+L +GR+ G E L +A ++LG G Sbjct: 182 ALGTTVVVVEQNVERALASADWVYILVAGRNLRDGAPAE-LAKLDMAAIFLGQSGG 236 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: 177 Number of extensions: 6 Number of successful extensions: 1 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: 254 Length adjustment: 24 Effective length of query: 223 Effective length of database: 230 Effective search space: 51290 Effective search space used: 51290 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