Align glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate GFF3407 PGA1_c34600 arginine biosynthesis bifunctional protein ArgJ
Query= BRENDA::Q92MJ1 (413 letters) >FitnessBrowser__Phaeo:GFF3407 Length = 409 Score = 386 bits (991), Expect = e-112 Identities = 220/417 (52%), Positives = 276/417 (66%), Gaps = 22/417 (5%) Query: 6 SPLAPKTFAEMPALRGVRMATAAAGIKYKNRTDVLMMLFDRPASVAGVFTRSKCPSAPVD 65 SPLAP F ++P + GVR A+AAAG+KYKNRTDV++ + D ++VAGVFTRS SAPV Sbjct: 6 SPLAPDHFPKLPQIAGVRFASAAAGVKYKNRTDVMLAVMDPGSAVAGVFTRSATRSAPVL 65 Query: 66 HCRQNLPGGI-----ARAVVVNSGNANAFTGKKGREATRLTAEAAAKAVGCSEAEVFLAS 120 C+ L A++VNSGN+NAFTG G+ + A G A VF AS Sbjct: 66 DCQAKLASNDNHTAHGAAILVNSGNSNAFTGHYGQTSVAEITRTVADITGIPAARVFTAS 125 Query: 121 TGVIGEPLD----ATKFAGVLDKLAASATQDFWFEAAKAIMTTDTYPKVATRSAEIGGVK 176 TGVIGEPL ++ A + D L A+A +D AA+AIMTTDT+ K A + E+GG Sbjct: 126 TGVIGEPLPHDRIVSQIATLNDGLVATAIED----AAEAIMTTDTFAKGAGATIEVGGKT 181 Query: 177 VAINGIAKGAGMIAPDMATMLSFVVTDADIAPAALQALLQAGVEPTFNSVTVDSDTSTSD 236 V+I GIAKG+GMIAPDMATML ++ TDA IA LQ LL + TFN +TVDSDTSTSD Sbjct: 182 VSIAGIAKGSGMIAPDMATMLVYIFTDAQIAQNDLQVLLSQICDRTFNCITVDSDTSTSD 241 Query: 237 TLMLFATGAAAGDGQAKVEDAADPRLDGFRAALDDLLRDLALQVVRDGEGARKMVEVTVE 296 +LML A+GA+ D + F AL++++ DL+ QVVRDGEGA K VE+ V Sbjct: 242 SLMLCASGASGIDVTGNTD---------FALALENVMLDLSHQVVRDGEGATKFVEIQVT 292 Query: 297 GAENDAAAKRIALSIANSPLVKTAVAGEDANWGRVVMAVGKSGEMAERDRLAIWFGDIRV 356 GA ND AK LSIANSPLVKTA+AGED NWGRVVMA+GKSG A+RD+L+I FG++ V Sbjct: 293 GAMNDHDAKVHGLSIANSPLVKTAIAGEDPNWGRVVMAIGKSGAAADRDKLSISFGEVLV 352 Query: 357 AVEGERDPAYSEAAATAVMQGETIPIRVDIGLGSGRATVYTCDLTKEYVEINGDYRS 413 A +G P Y E A M I I+VD+GL G++TV+TCDLT +Y+ IN DYRS Sbjct: 353 AEKGWVSPDYKETDGAAEMAKPEIVIKVDLGLAEGKSTVWTCDLTHQYISINADYRS 409 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: 444 Number of extensions: 15 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: 413 Length of database: 409 Length adjustment: 31 Effective length of query: 382 Effective length of database: 378 Effective search space: 144396 Effective search space used: 144396 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 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