Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate 3609962 Dshi_3343 aminotransferase class-III (RefSeq)
Query= curated2:O27392 (390 letters) >FitnessBrowser__Dino:3609962 Length = 413 Score = 192 bits (487), Expect = 2e-53 Identities = 136/392 (34%), Positives = 204/392 (52%), Gaps = 30/392 (7%) Query: 17 TYTRQPIVLSHGKGATVWDIEGNSYIDCFAGVAVNSIGHAHPKVALAICHQAQRLIHSSN 76 T+ P+ + G+G +WD G Y+DC+ V +GH HP+V AI QA R++++ Sbjct: 18 TFYDPPLHIVRGEGVWLWDAGGRRYLDCYNNVP--HVGHCHPRVVDAIARQA-RVLNTHT 74 Query: 77 IYYTREQVELAKLLTAISPH--DRVFFANSGAEANEGAIKLARKFTGKSEIIAAENSFHG 134 Y ++ + LT + D+ +G+EA + A+++AR TGK+ +IA +N++HG Sbjct: 75 RYLHEGVLDYIERLTGTMDNGLDQALLVCTGSEAVDVALRMARAATGKTGLIATDNTYHG 134 Query: 135 RTLATVTATGQKK----YSEPFR--PLPE-GFKHVPYGDIGAMADA----VGDETAAIIL 183 T A + ++ YS+ R P PE G +G A A A G AA+I+ Sbjct: 135 NTTAVAQLSTRRPPIGGYSDHVRLVPAPEPGTDGAAFGAHVARAAAELETAGHGVAALIV 194 Query: 184 EPVQGEGGVIIPPEGYLKDVQELARQNDVLLILDEVQTGFGRTGAMF-ASQLFGVEPDIT 242 P+ G+ P G+L+ R LLI DEVQ GFGR G +F Q G+ PD+ Sbjct: 195 CPIFANEGLPCLPRGFLEPAVAALRTRGGLLISDEVQPGFGRLGDVFWGYQALGIAPDVV 254 Query: 243 TVAKAMGGGYPIGAVLANERVAMAF-EPGDHGSTFGGNPWGCAAAIATIEVLMDEKLPER 301 T+ K+MG GYP+ V+A + AF E + +TFGG+P AAA+A ++VL DE L E Sbjct: 255 TLGKSMGNGYPVAGVVARTEIMGAFREAFGYFNTFGGSPVAAAAAMAVLDVLEDEGLVEN 314 Query: 302 AAKMGSYFLGRLRQVLHGCDAVRDIRGVGLMIGIEI---DGE-----CAGVVDAAREMGV 353 A ++G Y L RL+ + H A+ +RG GL +++ DG A V + A+ V Sbjct: 315 AKRVGRYTLERLQALRH--PAIDGVRGYGLAFALDLVDTDGAPNTALAAAVTEEAKRRSV 372 Query: 354 LINCTAG--KVIRIVPPLVIKKEEIDAAVDVL 383 LIN +++I PPL E D DVL Sbjct: 373 LINRIGRDMHILKIRPPLPFAPEHGDRLGDVL 404 Lambda K H 0.320 0.138 0.404 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: 450 Number of extensions: 22 Number of successful extensions: 7 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: 390 Length of database: 413 Length adjustment: 31 Effective length of query: 359 Effective length of database: 382 Effective search space: 137138 Effective search space used: 137138 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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