Align Acetylornithine aminotransferase; Short=ACOAT; EC 2.6.1.11 (characterized, see rationale)
to candidate CA265_RS15950 CA265_RS15950 glutamate-1-semialdehyde-2,1-aminomutase
Query= uniprot:A0A806JQF3 (400 letters) >FitnessBrowser__Pedo557:CA265_RS15950 Length = 456 Score = 125 bits (313), Expect = 3e-33 Identities = 99/300 (33%), Positives = 138/300 (46%), Gaps = 36/300 (12%) Query: 23 YGTPPIALASGDGAVVTDVDGRTYIDLLGGIAVNVLGHRHPAVIEAVTRQMSTLGHTSNL 82 YGTP + + GDG + D DG +ID G +LGH +P + E VT M N Sbjct: 57 YGTP-LFIEKGDGCYIWDADGNQFIDFCGSWGPLILGHNNPKIREKVTEVM------QNG 109 Query: 83 YATEPGIALAEELVALLGADQR--TRVFFCNSGAEANEAAFKLSR-LTGRTKLVAAHDAF 139 + AL EL L+ + R ++ F +SG EA +A +L+R T R K++ + Sbjct: 110 MSFGAPTALENELAELIIKNNRFVEKIRFTSSGTEAVMSAIRLARGFTSRDKILKFEGCY 169 Query: 140 HGR-------------TMGSLALTGQP---AKQTPFAPLPGDVTHVGYGDVDALAAAVDD 183 HG T G + G P A++T PL D T ++ A D Sbjct: 170 HGHSDSLLVKAGSGLVTFGETSSAGVPKSFAEETIVVPL-NDKT-----AIEQAFAQFKD 223 Query: 184 HTAAVFLEPIMGESGVVVPPAGYLAAARDITARRGALLVLDEVQTGMGRTGAFFAHQHDG 243 AAV +E I +G+++ Y+ R I G+LL+ DEV TG R G A H G Sbjct: 224 QIAAVIIEGIPANNGLIIQDEEYIHFLRKICTDNGSLLIFDEVITGF-RVGFEGAAAHYG 282 Query: 244 ITPDVVTLAKGLGGGLPIGACLAVGPAAELLTPG---LHGSTFGGNPVCAAAALAVLRVL 300 +TPD+VT K +GGGLP+G A ++P T GNPV AA +A L L Sbjct: 283 VTPDIVTYGKIIGGGLPVGMYGARAEIMAHISPDGGVYQAGTLSGNPVAMAAGIATLTEL 342 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: 363 Number of extensions: 18 Number of successful extensions: 3 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: 456 Length adjustment: 32 Effective length of query: 368 Effective length of database: 424 Effective search space: 156032 Effective search space used: 156032 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: 51 (24.3 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