Align glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate WP_012852502.1 TCUR_RS10645 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= BRENDA::P9WPZ3 (404 letters) >NCBI__GCF_000024385.1:WP_012852502.1 Length = 383 Score = 426 bits (1094), Expect = e-124 Identities = 233/389 (59%), Positives = 272/389 (69%), Gaps = 8/389 (2%) Query: 16 VTAPAGFRAAGVAAGIKASGALDLALVFNEGPDYAAAGVFTRNQVKAAPVLWTQQVLTTG 75 VTAP GFRAAGVAAGIK A DLALV N+GP AAAGVFTRN+VKAAPVLW+QQVL G Sbjct: 3 VTAPLGFRAAGVAAGIKGGEARDLALVVNDGPSRAAAGVFTRNRVKAAPVLWSQQVLRGG 62 Query: 76 RLRAVILNSGGANACTGPAGFADTHATAEAVAAALSDWGTETGAIEVAVCSTGLIGDRLP 135 R+RAV+LNSGGANACTG GF DTHATAE V L D A E+AVCSTGLIG+RLP Sbjct: 63 RVRAVVLNSGGANACTGAPGFQDTHATAEKVGQVLQD-----SAGEIAVCSTGLIGERLP 117 Query: 136 MDKLLAGVAHVVHEMHGGLVGGDEAAHAIMTTDNVPKQVALHHHDNWTVGGMAKGAGMLA 195 MDKLL + ++ GG AA AI TTD V K +A D +T+GGMAKGAGMLA Sbjct: 118 MDKLLPAIDVAAGQLSRD--GGLAAADAIRTTDKVAK-IAFRRADGYTIGGMAKGAGMLA 174 Query: 196 PSLATMLCVLTTDAAAEPAALERALRRAAAATFDRLDIDGSCSTNDTVLLLSSGASEIPP 255 PSLATMLCVLTTDA + AAL+RALR A A TFDRLD DG STNDTVLLL+SGAS P Sbjct: 175 PSLATMLCVLTTDADLDSAALDRALRAATAVTFDRLDTDGCISTNDTVLLLASGASGTTP 234 Query: 256 AQADLDEAVLRVCDDLCAQLQADAEGVTKRVTVTVTGAATEDDALVAARQIARDSLVKTA 315 +A+ + VC DL QL DAEG +K + + V GAA++ DA+ R IAR++L+K A Sbjct: 235 DEAEFTALLTEVCADLTRQLLNDAEGASKTIAIEVVGAASDFDAVTVGRAIARNNLLKCA 294 Query: 316 LFGSDPNWGRVLAAVGMAPITLDPDRISVSFNGAAVCVHGVGAPGAREVDLSDADIDITV 375 + G DPNWGRVLAAVG +PD+I+V+ NG VC G +VDLS ++ ITV Sbjct: 295 IHGEDPNWGRVLAAVGSTEAVFEPDKINVAINGVWVCRGGAVGDDRGKVDLSPREVTITV 354 Query: 376 DLGVGDGQARIRTTDLSHAYVEENSAYSS 404 DL G A + TTDL+ YV ENSAYS+ Sbjct: 355 DLSAGPASATVWTTDLTAEYVHENSAYST 383 Lambda K H 0.317 0.131 0.380 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: 515 Number of extensions: 20 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: 404 Length of database: 383 Length adjustment: 31 Effective length of query: 373 Effective length of database: 352 Effective search space: 131296 Effective search space used: 131296 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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