Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_106714946.1 CU100_RS02400 aspartate aminotransferase family protein
Query= curated2:O27392 (390 letters) >NCBI__GCF_003010935.1:WP_106714946.1 Length = 441 Score = 187 bits (475), Expect = 5e-52 Identities = 142/421 (33%), Positives = 208/421 (49%), Gaps = 52/421 (12%) Query: 18 YTRQPIVLSHGKGATVWDIEGNSYIDCFAGVAVNSIGHAHPKVALAICHQAQRLIHSSNI 77 + P +L K +G +D AG+ + GH P++ A+ Q L ++ Sbjct: 24 FKENPRLLVSAKDMHYKSHDGREILDGTAGLWCCNAGHGRPRIVEAVQKQVAELDYAPAF 83 Query: 78 YYTREQV-ELAKLLTAI--SPHDRVFFANSGAEANEGAIKLARKFTG------KSEIIAA 128 + ELA L A+ SP D VFF NSG+E+ + A+K+A + K ++I Sbjct: 84 QMGHPKAFELAARLAAMLPSPLDHVFFTNSGSESVDTALKIALAYHRAKGNGTKVKLIGR 143 Query: 129 ENSFHGRTLATVTATGQKKYSEPFRPLPEGFKHV----------------PYG------- 165 E +HG ++ G + F G H+ YG Sbjct: 144 ERGYHGVGFGGISVGGISGNRKTFGNALSGIDHIRHTHDLARNAYTRGEPEYGAEFADDL 203 Query: 166 -DIGAMADAVGDETAAIILEPVQGEGGVIIPPEGYLKDVQELARQNDVLLILDEVQTGFG 224 + A+ DA AA+I+EPV G GV+IPP+GYLK ++E+ ++D+LLI DEV TGFG Sbjct: 204 EKVVALHDA--SNIAAVIVEPVAGSTGVLIPPKGYLKRLREICTKHDILLIFDEVITGFG 261 Query: 225 RTGAMFASQLFGVEPDITTVAKAMGGG-YPIGAVLANERVAMAFEPGD-------HGSTF 276 R G FA FGV PD+ T AK + G P+GAV A++++ F G HG T+ Sbjct: 262 RLGTPFAVDYFGVVPDLVTTAKGITSGVIPMGAVFASKQIYETFMTGAENMIELFHGYTY 321 Query: 277 GGNPWGCAAAIATIEVLMDEKLPERAAKMGSYFLGRLRQVLHGCDAVRDIRGVGLMIGIE 336 G+P CAAA+AT++ +E L RA+++ Y+ L L G V DIR +GL+ IE Sbjct: 322 SGHPVACAAALATLDTYEEEGLLTRASEISGYWEEAL-HALKGLPHVIDIRNLGLIGAIE 380 Query: 337 IDG-ECAGVVDA------AREMGVLINCTAGKVIRIVPPLVIKKEEIDAAVDVLGHVISD 389 ++ E A A A E GVLI T G +I + PPL+I K +I+ D L V+ + Sbjct: 381 LEPIEGAPTKRAFQAFLKAYEKGVLIR-TTGDIIALSPPLIISKGQIEHLFDTLADVLKN 439 Query: 390 L 390 L Sbjct: 440 L 440 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: 460 Number of extensions: 33 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: 441 Length adjustment: 31 Effective length of query: 359 Effective length of database: 410 Effective search space: 147190 Effective search space used: 147190 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 Jul 26 2024. The underlying query database was built on Jul 25 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