Align glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate YP_425486.1 Rru_A0394 N-acetylglutamate synthase / glutamate N-acetyltransferase
Query= BRENDA::Q92MJ1 (413 letters) >NCBI__GCF_000013085.1:YP_425486.1 Length = 412 Score = 447 bits (1149), Expect = e-130 Identities = 242/415 (58%), Positives = 294/415 (70%), Gaps = 5/415 (1%) Query: 1 MSGSVSPLAPKTFAEMPALRGVRMATAAAGIKYKNRTDVLMMLFDRPASVAGVFTRSKCP 60 M+ +VSPLAP F +PA+ GV +AT G++Y+ R D+L++ ++ AGVFTRSK Sbjct: 1 MTHAVSPLAPAAFPALPAIAGVDLATHNTGLRYQGRPDLLVVRLAAGSTGAGVFTRSKTR 60 Query: 61 SAPVDHCRQNLP--GGIARAVVVNSGNANAFTGKKGREATRLTAEAAAKAVGCSEAEVFL 118 SAPVD CR+ L GG AR +VVNSGNANAFTG +G + T +AA A+ C EVF+ Sbjct: 61 SAPVDWCRRALAAGGGAARGLVVNSGNANAFTGSRGIASVERTIASAAMALSCPPEEVFI 120 Query: 119 ASTGVIGEPLDATKFAGVLDKLAASATQDFWFEAAKAIMTTDTYPKVATRSAEIGGVKVA 178 ASTG IG PLD K ++D +A S WF+AA AI TTDTYPK ATR+A I GV V Sbjct: 121 ASTGTIGVPLDDAKITTLIDAIAPSLGTASWFDAATAISTTDTYPKGATRTATIDGVSVT 180 Query: 179 INGIAKGAGMIAPDMATMLSFVVTDADIAPAALQALLQAGVEPTFNSVTVDSDTSTSDTL 238 ++GIAKG+GMIAPDMATML++V TDA + LQ LL GVE +FN++TVD DTSTSD+L Sbjct: 181 LSGIAKGSGMIAPDMATMLAYVFTDAALPAGVLQDLLTQGVERSFNAITVDGDTSTSDSL 240 Query: 239 MLFATGAAAGDGQAKVEDAADPRLDGFRAALDDLLRDLALQVVRDGEGARKMVEVTVEGA 298 MLFATG A G A V+ A D RL GFR AL LL DLA QVVRDGEGA K V VTV GA Sbjct: 241 MLFATGKA---GNAPVQTALDRRLSGFRKALFALLTDLAHQVVRDGEGATKFVTVTVTGA 297 Query: 299 ENDAAAKRIALSIANSPLVKTAVAGEDANWGRVVMAVGKSGEMAERDRLAIWFGDIRVAV 358 ++ AAKRI L+IANSPLVKTA+AGEDANWGR+VMAVGKSGE A+RDRL I G +A Sbjct: 298 KSPRAAKRIGLAIANSPLVKTAIAGEDANWGRIVMAVGKSGEEADRDRLEIRIGGHLIAA 357 Query: 359 EGERDPAYSEAAATAVMQGETIPIRVDIGLGSGRATVYTCDLTKEYVEINGDYRS 413 EG+ Y E M+G + I VD+GLG G+ATV+TCDLT Y++IN DYR+ Sbjct: 358 EGQAVADYDEGPVATHMKGTDVDIAVDLGLGRGKATVWTCDLTHGYIDINADYRT 412 Lambda K H 0.316 0.130 0.365 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: 455 Number of extensions: 15 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: 413 Length of database: 412 Length adjustment: 31 Effective length of query: 382 Effective length of database: 381 Effective search space: 145542 Effective search space used: 145542 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: 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