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_035702265.1 BA79_RS08570 sugar ABC transporter ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_000691145.1:WP_035702265.1 Length = 493 Score = 113 bits (282), Expect = 8e-30 Identities = 65/215 (30%), Positives = 119/215 (55%), Gaps = 7/215 (3%) Query: 12 LEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITF 71 +E+ N+H + K+ +L GV+F + +GE+ ++G NGAGKSTL + GL + G I Sbjct: 3 IEMHNIHKAFGKNT-VLAGVSFDLVTGEVHALMGENGAGKSTLMNLLTGLYSLDQGTIQI 61 Query: 72 KGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRND----SLQPLKDKIF 127 GK A + + G+ ++ Q N++P ++V ENL +G I + +K Sbjct: 62 DGKETAFKNPKEAEQNGIAFIHQELNIWPDMTVLENLFIGKEIYTKLGLLDTKKMKALAQ 121 Query: 128 AMFPRLSDRRR--QRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQ 185 A RLS Q AG+ S G++QM+ + KALM + ++++DEP+AAL+ + ++F+ Sbjct: 122 AQLDRLSVNLSLDQEAGSCSVGQKQMIEIAKALMTDAKVIIMDEPTAALTDREIEKLFQV 181 Query: 186 VKQINQEGTAIILVEQNARKALEMADRGYVLESGR 220 ++ + +EG +I+ + + + DR ++ G+ Sbjct: 182 IESLKKEGVSIVYISHRMEEIFAICDRITIMRDGK 216 Score = 82.4 bits (202), Expect = 2e-20 Identities = 60/215 (27%), Positives = 107/215 (49%), Gaps = 27/215 (12%) Query: 29 QGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITFKGKNIAGLKSNQIVRLG 88 Q V+F V++GE+V V G GAG++ + +++FGL G+I GK K + V+LG Sbjct: 268 QDVSFSVKAGEIVGVAGLMGAGRTEMMRSLFGLDPLDQGEIWVHGKKAVIKKPSDAVKLG 327 Query: 89 MCYVPQIANVFPSLSVEENLEMGAFIRN-------DSLQPL--------KDKIFAMFPRL 133 + ++ + +E L + A IR DS P +D + + RL Sbjct: 328 IGFITEDRK-------DEGLMLDASIRENIGLPNLDSFSPKGLIDKKNEQDFVDLLIKRL 380 Query: 134 SDRRRQR---AGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQIN 190 + + A +LSGG +Q + + K + ++P +L+LDEP+ + ++++ + ++ Sbjct: 381 TIKTASSEISARSLSGGNQQKVVIAKWIGIQPKVLILDEPTRGVDVGAKREIYQLMNELT 440 Query: 191 QEGTAIILVEQNARKALEMADRGYVLESGRDAISG 225 G AI++V + L M+DR V+ G ISG Sbjct: 441 DRGVAILMVSSELPEVLGMSDRVLVIHEG--TISG 473 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: 319 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 247 Length of database: 493 Length adjustment: 29 Effective length of query: 218 Effective length of database: 464 Effective search space: 101152 Effective search space used: 101152 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: 49 (23.5 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