Align glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate CCNA_03162 CCNA_03162 bifunctional ornithine acetyltransferase/N-acetylglutamate synthase
Query= BRENDA::Q92MJ1 (413 letters) >FitnessBrowser__Caulo:CCNA_03162 Length = 481 Score = 398 bits (1023), Expect = e-115 Identities = 218/413 (52%), Positives = 279/413 (67%), Gaps = 7/413 (1%) Query: 4 SVSPLAPKTFAEMPALRGVRMATAAAGIKYKNRTDVLMMLFDRPASVAGVFTRSKCPSAP 63 ++SPLA F +P + GV +AT AG R D+L+M F S AGVFTR SAP Sbjct: 73 AISPLAVP-FPTIPPIAGVEIATGRAGFYKHEREDLLLMRFAEGTSAAGVFTRHGVGSAP 131 Query: 64 VDHCRQNLP---GGIARAVVVNSGNANAFTGKKGREATRLTAEAAAKAVGCSEAEVFLAS 120 VD C++ L G RA+VVN+G AN+FTGK G +A R A A K C + +V +AS Sbjct: 132 VDWCKRQLAATGGADVRALVVNAGCANSFTGKPGADAVRRVATAVGKRFDCRQRDVMMAS 191 Query: 121 TGVIGEPLDATKFAGVLDKLAASATQDFWFEAAKAIMTTDTYPKVATRSAEIGGVKVAIN 180 TGVIG LD +K L ++ + D W EA +AIMTTDT+PK A +A I G +V I Sbjct: 192 TGVIGVILDDSKITARLPEVESRLKADAWAEAGRAIMTTDTFPKGAYATAVIDGHEVKIA 251 Query: 181 GIAKGAGMIAPDMATMLSFVVTDADIAPAALQALLQAGVEPTFNSVTVDSDTSTSDTLML 240 GIAKG+GMIAPDMATML+FV TDA IAPAALQ L+ TFN VTVD D ST+DTL+L Sbjct: 252 GIAKGSGMIAPDMATMLAFVATDAAIAPAALQTLVSLYTRTTFNCVTVDGDRSTNDTLLL 311 Query: 241 FATGAAAGDGQAKVEDAADPRLDGFRAALDDLLRDLALQVVRDGEGARKMVEVTVEGAEN 300 FATG + G K+ A D RL FR L+ +L DLALQ+V+DGEGA K V++TV GAE+ Sbjct: 312 FATGQS---GAPKIHRAGDKRLADFREKLEGVLLDLALQLVKDGEGATKFVKITVNGAES 368 Query: 301 DAAAKRIALSIANSPLVKTAVAGEDANWGRVVMAVGKSGEMAERDRLAIWFGDIRVAVEG 360 A+A++IA +IA SPLVKTA AGEDANWGR+VMAVG++ E R+++++ FGD+ A +G Sbjct: 369 PASARKIARTIAESPLVKTAFAGEDANWGRIVMAVGRADEPVAREKISVKFGDLYAARDG 428 Query: 361 ERDPAYSEAAATAVMQGETIPIRVDIGLGSGRATVYTCDLTKEYVEINGDYRS 413 Y EA +A ++ + + VD+G+G G ATV+TCDLTK+YV INGDYRS Sbjct: 429 LISAEYDEAKMSAYVKNQAFEVSVDVGVGRGSATVWTCDLTKQYVAINGDYRS 481 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: 495 Number of extensions: 18 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: 481 Length adjustment: 32 Effective length of query: 381 Effective length of database: 449 Effective search space: 171069 Effective search space used: 171069 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 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