Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate AZOBR_RS31120 AZOBR_RS31120 adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= curated2:Q8TUZ5 (389 letters) >FitnessBrowser__azobra:AZOBR_RS31120 Length = 434 Score = 190 bits (483), Expect = 6e-53 Identities = 144/413 (34%), Positives = 212/413 (51%), Gaps = 55/413 (13%) Query: 19 PVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNL-YYN 77 P+ + G+GA ++ ++G E +DL++ VN+ GH HPAV A+ EQ RL + + Sbjct: 25 PLAVTHGKGASLFTEDGREILDLISSWWVNLHGHAHPAVAGAIAEQAHRLEQVIFADFTH 84 Query: 78 EPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFTGCT------KFIAFEGGF 131 P A A LAE P L +VF+ ++G+ +VE A+KLA ++ +F+AFEG + Sbjct: 85 SPAARLAARLAEVLPGGLGRVFYSDNGSTAVEVALKLAWQYWRNKGEGQRRRFLAFEGSY 144 Query: 132 HGRTMGALSATWKPEFREPFEPLVPEFEHVPY-----GD--VNAVEKAIDD--------- 175 HG T GA++A F PF+ L+ + +PY GD V A E A D Sbjct: 145 HGDTFGAMAAGVGSGFYAPFQELLFAVDRMPYPATWDGDPEVEAKEAAALDWLDRWLATN 204 Query: 176 --DTAAVIVEP-VQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFE 232 + AVI+EP VQG +G+R FLR + G L+I DEV +G GRTG FA + Sbjct: 205 GAELVAVIIEPLVQGASGMRFCRPEFLRAMAARVRAAGGLVIFDEVMTGFGRTGALFASQ 264 Query: 233 HEDVLPDIVCLAKGLGGG-VPVGATIAREEVAEAF------EPGDHGSTFGGNPLACAAV 285 V PD++CL+KGL GG +P+ T + EAF HG +F NPL CAA Sbjct: 265 KAGVAPDLICLSKGLTGGFLPLSVTACGASIYEAFLGAGFDRAFAHGHSFTANPLGCAAA 324 Query: 286 CAAVSTVLEENLPEAAERKGKLAMRILSEAEDVVEEVRG-----RGLMMG----VEVGDD 336 A++ L +AE LA RI + + ++ G RG +MG +EV D Sbjct: 325 LASL------ELTTSAETTANLA-RIETRHRAAIADLSGHPKLSRGRVMGTIAAIEVTDA 377 Query: 337 ER-----AKDVAREMLDRGALVNVTSGDVIRLVPPLVIGEDELEKALAELADA 384 + + + R L+RG L+ G VI L+PP + + +L++A A + DA Sbjct: 378 QGYTAAVGQTLKRFFLERGLLLR-PLGPVIYLLPPYCVTDGQLDRAYAAIRDA 429 Lambda K H 0.318 0.137 0.405 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: 412 Number of extensions: 25 Number of successful extensions: 6 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: 389 Length of database: 434 Length adjustment: 31 Effective length of query: 358 Effective length of database: 403 Effective search space: 144274 Effective search space used: 144274 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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