Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate 208688 DVU3168 glutamate-1-semialdehyde-2,1-aminomutase
Query= curated2:P36839 (385 letters) >MicrobesOnline__882:208688 Length = 423 Score = 152 bits (384), Expect = 2e-41 Identities = 110/308 (35%), Positives = 160/308 (51%), Gaps = 17/308 (5%) Query: 15 IKKAKGTYVEDQNGKTYLDFIQGIAVSNLGHCHEAVTEAVKKQLDSVWHVSNLFQNSLQE 74 I +A G+ + +G+T++DF++ LGH H VT AV +D ++ + Sbjct: 37 IARAAGSRLHTVDGETFIDFVESWGPMLLGHTHPEVTAAVHAAVDRGTSYGAPCEDEVV- 95 Query: 75 QAAQKLAAHSAGDLVFFCNSGAEANEGAIKLARKATGKTKIITFLQSFHGRTYAGMAATG 134 AA+ + A D+V NSG EA A++LAR TG+TK++ F+ +HG +A+ G Sbjct: 96 LAAKVVDALPGVDMVRMVNSGTEATMSALRLARGYTGRTKLVKFVGCYHGHADPFLASAG 155 Query: 135 QDKIKTGFGPMLGGFH--------YLPYNDPSAFKALG--EEGDIAAVMLETVQGEGGVN 184 + T P G PYND +A K L DIAA+++E V G G+ Sbjct: 156 SG-VATLSIPGTPGVPESTVRDTLLAPYNDLAAVKDLFALHGKDIAAIIVEAVAGNMGLV 214 Query: 185 PASAEFLSAVQSFCKEKQALLIIDEIQTGIGRTGKGFAYEHFGLSPDIITVAKGLGNGFP 244 P A FL ++ C + ALLI DE+ TG R G A + FG++PD+ T+ K +G G P Sbjct: 215 PPKAGFLEGLRELCDQHGALLIFDEVITGF-RVSFGGAQQRFGITPDLTTLGKIIGGGLP 273 Query: 245 VGAVIGKKQLGEAFTPGS---HGTTFGGNMLAMAAVNATLQIVFQPDFLQEAADKGAFLK 301 VGA GK+++ + P T GN LAMAA ATL ++ + D+ A AF+K Sbjct: 274 VGAYGGKREIMQRIAPCGEVYQAGTLSGNPLAMAAGIATLDVLSRSDYAGLEARVAAFVK 333 Query: 302 EQLEAELK 309 E LEA LK Sbjct: 334 E-LEAILK 340 Lambda K H 0.318 0.135 0.390 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: 378 Number of extensions: 17 Number of successful extensions: 5 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: 385 Length of database: 423 Length adjustment: 31 Effective length of query: 354 Effective length of database: 392 Effective search space: 138768 Effective search space used: 138768 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 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