Align Acetylornithine aminotransferase; Short=ACOAT; EC 2.6.1.11 (characterized, see rationale)
to candidate WP_025274361.1 HALAL_RS0112700 acetylornithine transaminase
Query= uniprot:A0A806JQF3 (400 letters) >NCBI__GCF_000527155.1:WP_025274361.1 Length = 401 Score = 375 bits (962), Expect = e-108 Identities = 201/399 (50%), Positives = 262/399 (65%), Gaps = 10/399 (2%) Query: 1 MTGASTTTATMRQRWQAVMMNNYGTPPIALASGDGAVVTDVDGRTYIDLLGGIAVNVLGH 60 MT STT ++ R+ +M+ YG PP+ALASG+G VTDVDGRTY+D++GGIAV+ +GH Sbjct: 1 MTTDSTTA--LQNRYADALMDTYGQPPVALASGNGRHVTDVDGRTYLDMIGGIAVSTVGH 58 Query: 61 RHPAVIEAVTRQMSTLGHTSNLYATEPGIALAEELVALLGADQRTRVFFCNSGAEANEAA 120 RHP +EAV RQ +T+ HTSNL+ + LAE LV L GAD R VFF NSG EANEAA Sbjct: 59 RHPDYVEAVVRQTATIAHTSNLFFHPTEVELAETLVKLTGADGR--VFFSNSGTEANEAA 116 Query: 121 FKLS----RLTGRTKLVAAHDAFHGRTMGSLALTGQPAKQTPFAPLPGDVTHVGYGDVDA 176 KL+ + G+T++VAA ++FHGRT+G+LA+TG+ + + PFAP + T V YGD A Sbjct: 117 LKLALKAGKPHGKTRIVAAENSFHGRTLGTLAVTGKASIREPFAPFGIEATFVPYGDTAA 176 Query: 177 LAAAVDDHTAAVFLEPIMGESGVVVPPAGYLAAARDITARRGALLVLDEVQTGMGRTGAF 236 L AAVDD AAV LEP GE+GVV +L AR +T G+ L+LDE+Q G GRTG + Sbjct: 177 LTAAVDDTVAAVILEPTQGEAGVVPASTDFLHTARALTHEHGSALILDEIQAGFGRTGRW 236 Query: 237 FAHQHDGITPDVVTLAKGLGGGLPIGACLAVGPAAELLTPGLHGSTFGGNPVCAAAALAV 296 FAH ITPD++TLAKGL GG+P+GA + VG + G HGSTFGGNP+ AAALAV Sbjct: 237 FAHHAADITPDIITLAKGLAGGIPMGATIGVGDWGNVFQAGDHGSTFGGNPIAGAAALAV 296 Query: 297 LRVLASDGLVRRAEVLGKSLRHGIEALGHPLIDHVRGRGLLLGIALTAPHAKDAEATARD 356 + ++ + L LG+ L + + HP + VRG L GI L A D R+ Sbjct: 297 IDIIEREDLFDNVNTLGRKLENRLH--NHPAVIAVRGEALWRGIVLDTDIAADVCGQLRN 354 Query: 357 AGYLVNAAAPDVIRLAPPLIIAEAQLDGFVAALPAILDR 395 AG L N P+VIR+APPL I A+L+ F +AL +LD+ Sbjct: 355 AGILANPVRPNVIRIAPPLSITAAELEQFTSALTDVLDQ 393 Lambda K H 0.320 0.136 0.399 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: 490 Number of extensions: 29 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: 400 Length of database: 401 Length adjustment: 31 Effective length of query: 369 Effective length of database: 370 Effective search space: 136530 Effective search space used: 136530 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