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 5207910 Shew_0426 ABC transporter-related protein (RefSeq)
Query= TCDB::Q8YT15 (247 letters) >FitnessBrowser__PV4:5207910 Length = 340 Score = 104 bits (259), Expect = 3e-27 Identities = 69/203 (33%), Positives = 112/203 (55%), Gaps = 5/203 (2%) Query: 31 VNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITFKGKNIAGLKSNQIVRLGMC 90 ++ +V+ G + +GPNG GKST + + GLLTP G+I+ G I + + +R + Sbjct: 27 LDLQVQKGHIYGFLGPNGCGKSTTIRMLTGLLTPTRGEISVLGMAIP--QQAEALRRRIG 84 Query: 91 YVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAMFP--RLSDRRRQRAGTLSGGE 148 Y+ Q +++ LSV ENL+ A I + K KI + L +R+Q AGTLSGG+ Sbjct: 85 YMTQKFSLYEDLSVRENLQFIADIYGLGARESKRKIDELIDTYHLDAQRQQLAGTLSGGQ 144 Query: 149 RQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQINQEGTAIILVEQNARKALE 208 +Q L + A + EP LL LDEP++A+ P +EQ+ +++ GT+I++ +A + Sbjct: 145 KQRLGLACACINEPELLFLDEPTSAVDPQNRRDFWEQLFDLSERGTSILVTTHYMDEA-Q 203 Query: 209 MADRGYVLESGRDAISGPGQELL 231 + ++ESG G Q LL Sbjct: 204 RCHQLAIMESGHIRAKGNPQALL 226 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: 216 Number of extensions: 9 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: 340 Length adjustment: 26 Effective length of query: 221 Effective length of database: 314 Effective search space: 69394 Effective search space used: 69394 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: 48 (23.1 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