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 209035 DVU0105 glutamine ABC transporter, ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >MicrobesOnline__882:209035 Length = 244 Score = 132 bits (333), Expect = 5e-36 Identities = 85/241 (35%), Positives = 137/241 (56%), Gaps = 5/241 (2%) Query: 9 TPLLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGK 68 TP++E+ N+H Y D +L+G++ V +GE+V VIGP+G+GKST + I L +G Sbjct: 2 TPMIEIRNLHKSY-GDHHVLRGIDLTVRTGEVVVVIGPSGSGKSTALRCINRLEEITSGT 60 Query: 69 ITFKGKNIAGLKSN-QIVRLGMCYVPQIANVFPSLSVEENLEMGAF-IRNDSLQPLKDKI 126 I G ++ K++ VR V Q N+FP +SV EN+ +G +R + Q + Sbjct: 61 IIVDGYDLYDPKTDINHVRTEAGMVFQQFNLFPHMSVLENVTIGPVKVRRMARQEAQALG 120 Query: 127 FAMFPR--LSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFE 184 A+ + L+D+ LSGG++Q +A+ ++L ++P +L+ DEP++AL P LV +V E Sbjct: 121 LALLEKVGLADKAHAYPDQLSGGQKQRVAIARSLAMQPKVLLFDEPTSALDPELVGEVLE 180 Query: 185 QVKQINQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLGAG 244 +KQ+ +EG +++V A E+ADR ++ G+ GP EL DPK L G Sbjct: 181 VMKQLAREGMTMVVVTHEMGFAREVADRVIFIDYGKIQEEGPPNELFADPKNPRLREFLG 240 Query: 245 K 245 K Sbjct: 241 K 241 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: 146 Number of extensions: 7 Number of successful extensions: 4 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: 244 Length adjustment: 24 Effective length of query: 223 Effective length of database: 220 Effective search space: 49060 Effective search space used: 49060 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