Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_011653767.1 RL_RS22620 ornithine--oxo-acid transaminase
Query= curated2:O27392 (390 letters) >NCBI__GCF_000009265.1:WP_011653767.1 Length = 399 Score = 305 bits (780), Expect = 2e-87 Identities = 167/397 (42%), Positives = 234/397 (58%), Gaps = 14/397 (3%) Query: 3 SEEIIELERKFIMQTYTRQPIVLSHGKGATVWDIEGNSYIDCFAGVAVNSIGHAHPKVAL 62 SE++I E++ Y +VL+ G+G VWD +GN Y+DC + + + GH HPK+ Sbjct: 4 SEKLIATEQRLGAHNYKPLDVVLTRGEGVYVWDTDGNRYLDCLSAYSAVNQGHCHPKILA 63 Query: 63 AICHQAQRLIHSSNIYYTREQVELAKLLTAISPHDRVFFANSGAEANEGAIKLARKF--- 119 A+ QA RL +S + + L + L A++ ++ NSGAEA E AIK RK+ Sbjct: 64 AMVEQAGRLTLTSRAFRNDQLAYLYEELAALTGSHKILPMNSGAEAVETAIKAVRKWGYE 123 Query: 120 -----TGKSEIIAAENSFHGRTLATVTATGQKKYSEPFRPLPEGFKHVPYGDIGAMADAV 174 GK+EII ++FHGRTL+ ++ + + F P GF+ +P+G+ A A A+ Sbjct: 124 VKGVPEGKAEIIVCADNFHGRTLSIISFSTDPEARTGFGPYTPGFRIIPFGNAEAFAAAI 183 Query: 175 GDETAAIILEPVQGEGGVIIPPEGYLKDVQELARQNDVLLILDEVQTGFGRTGAMFASQL 234 T A ++EP+QGE GVIIPP GY ++EL N+V LILDE+QTG GRTG + A + Sbjct: 184 NANTVAALIEPIQGEAGVIIPPAGYFTRIRELCTANNVTLILDEIQTGLGRTGKLLAEEH 243 Query: 235 FGVEPDITTVAKAMGGG-YPIGAVLANERVAMAFEPGDHGSTFGGNPWGCAAAIATIEVL 293 G+E D+T + KA+ GG YP+ AVL+N V +PG HGSTFGGNP CA A A ++VL Sbjct: 244 EGIEADVTLIGKALSGGFYPVSAVLSNSEVLGVLKPGQHGSTFGGNPLACAVARAALKVL 303 Query: 294 MDEKLPERAAKMGSYFLGRLRQVLHGCDAVRDIRGVGLMIGIEIDGECAGV---VDAARE 350 +E + E AA MG YF LR + + VRD+RG GLM+ IE+ E G A +E Sbjct: 304 TEEGMIENAAVMGDYFTEGLRSI--RSNIVRDVRGRGLMMAIELVPEAGGARQYCHALKE 361 Query: 351 MGVLINCTAGKVIRIVPPLVIKKEEIDAAVDVLGHVI 387 G+L T IR+ PPLVI KE++D AV + I Sbjct: 362 RGLLAKDTHDHTIRLAPPLVITKEQVDWAVSQIEKTI 398 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: 425 Number of extensions: 25 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: 390 Length of database: 399 Length adjustment: 31 Effective length of query: 359 Effective length of database: 368 Effective search space: 132112 Effective search space used: 132112 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 10 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