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 3610347 Dshi_3728 ABC transporter related (RefSeq)
Query= TCDB::Q8YT15 (247 letters) >FitnessBrowser__Dino:3610347 Length = 236 Score = 170 bits (431), Expect = 2e-47 Identities = 88/217 (40%), Positives = 136/217 (62%), Gaps = 2/217 (0%) Query: 10 PLLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKI 69 P+L +EN+H+ Y ++QGV+ V GE++ V G NG GK+TL K I G + P +G I Sbjct: 4 PMLSIENLHSHYGLS-HVIQGVSLDVGRGEILGVFGRNGVGKTTLLKNIAGWVKPSSGSI 62 Query: 70 TFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAF-IRNDSLQPLKDKIFA 128 GK I G + + I R G+ VP+ +FP L+V+ENLE+G ++ + D + Sbjct: 63 RMDGKQIGGDEPDAINRAGLAIVPEDRRIFPGLTVQENLELGLLGLKGPKPRSKLDPVLE 122 Query: 129 MFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQ 188 FPRL++R +Q A TLSGGE+QMLAM + ++ EP +++DEPS L+P++V ++F +++ Sbjct: 123 RFPRLAERAQQPATTLSGGEQQMLAMARIMVAEPRAVLIDEPSEGLAPMIVAEIFAILRE 182 Query: 189 INQEGTAIILVEQNARKALEMADRGYVLESGRDAISG 225 + G AI+LVEQN +AL + DR ++E G G Sbjct: 183 MKDAGCAIVLVEQNIHEALSICDRFVLVERGAIVFEG 219 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: 181 Number of extensions: 11 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: 236 Length adjustment: 23 Effective length of query: 224 Effective length of database: 213 Effective search space: 47712 Effective search space used: 47712 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