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 3608115 Dshi_1520 ABC transporter related (RefSeq)
Query= TCDB::Q8YT15 (247 letters) >FitnessBrowser__Dino:3608115 Length = 277 Score = 232 bits (591), Expect = 7e-66 Identities = 108/233 (46%), Positives = 162/233 (69%) Query: 10 PLLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKI 69 P L + + GY DIL V+ GE+ ++GPNGAGKST K +FG+L HTG + Sbjct: 44 PFLIGDGMTGGYGSGADILHDCTLAVDRGEIAVIVGPNGAGKSTAMKAVFGMLNIHTGSV 103 Query: 70 TFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAM 129 G++I GL V GM +VPQ+ N+F +++VEENLEMGAF+R D + ++++ + Sbjct: 104 RLDGEDITGLSPQARVAKGMAFVPQVNNIFTTMTVEENLEMGAFLRRDDISETMEQVYEL 163 Query: 130 FPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQI 189 FP L ++RRQ AG LSGG+RQ +A+G+ALM P +L+LDEP+A +SPI++ ++F+++ ++ Sbjct: 164 FPILREKRRQAAGELSGGQRQQVAVGRALMTRPQVLMLDEPTAGVSPIVMDELFDRIIEV 223 Query: 190 NQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLG 242 + G +I++VEQNAR+ALE+AD+GYVL GR+ + GQ LL DP V + +LG Sbjct: 224 ARTGISILMVEQNARQALEIADKGYVLVQGRNRYTDTGQALLADPDVRKSFLG 276 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: 214 Number of extensions: 8 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: 277 Length adjustment: 25 Effective length of query: 222 Effective length of database: 252 Effective search space: 55944 Effective search space used: 55944 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: 47 (22.7 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