Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate 3608039 Dshi_1446 aminotransferase class-III (RefSeq)
Query= curated2:Q8TUZ5 (389 letters) >FitnessBrowser__Dino:3608039 Length = 444 Score = 212 bits (540), Expect = 1e-59 Identities = 146/421 (34%), Positives = 213/421 (50%), Gaps = 56/421 (13%) Query: 21 TLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHC-SNLYYNEP 79 T V G G + D +G Y+D G AV+ LGH HPAV A+ Q++++ + + +EP Sbjct: 15 TAVAGAGCYIIDADGKRYLDGSGGAAVSCLGHDHPAVRAALHAQIDKIAFAHTGFFTSEP 74 Query: 80 QAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFTGCT------KFIAFEGGFHG 133 L AAPK + KV+ + G+ESVE A+KLAR+F T + IA +HG Sbjct: 75 AEVLCDALIAAAPKGIEKVYLLSGGSESVEAALKLARQFFLETGEPRRHRVIARRQSYHG 134 Query: 134 RTMGALSATWKPEFREPFEPLVPE---------FEHVPYGDVNA-------------VEK 171 T+GAL+A RE + PL+ E + H G+ +A +E+ Sbjct: 135 NTLGALAAGGNAWRREKYAPLLVETYHIDPCYAYRHQAVGESDAAYGRRAADALRTEIER 194 Query: 172 AIDDDTAAVIVEPVQGEAGVRIPPE-GFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFA 230 + A I EPV G +PP G+ +RE+CDE+G+LLI+DEV GMGRTG FA Sbjct: 195 LGPETVMAFIAEPVVGATAGAVPPAPGYFERIREICDEYGVLLILDEVMCGMGRTGTLFA 254 Query: 231 FEHEDVLPDIVCLAKGLGGG-VPVGATIAREEVAEAFEPG----DHGSTFGGNPLACAAV 285 E + + PDIV +AKGLG G P+GA +A + +A G HG T+ G+PLA AA Sbjct: 255 CEQDGISPDIVTIAKGLGAGYAPIGAMLASGRIYDAIAQGSGSFQHGHTYHGHPLAAAAA 314 Query: 286 CAAVSTVLEENLPEAAERKGKLAMRILSEA---EDVVEEVRGRGLMMGVEVGDD---ERA 339 A V T+ KG L A V ++RGRGL G+E+ +D +R Sbjct: 315 GAVVETLRAPGTMAQVRAKGATLQSRLEAALGQHSHVGDIRGRGLFRGIELVEDRDTKRP 374 Query: 340 KDVAREM--------LDRGAL-------VNVTSGDVIRLVPPLVIGEDELEKALAELADA 384 D AR++ + RG + ++ GD I L PP +I + +++ + LA+A Sbjct: 375 LDPARKVSARIKAAAMARGLICYPGSGTIDGKHGDHILLAPPFIIEDKQIDALVHMLAEA 434 Query: 385 L 385 + Sbjct: 435 I 435 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: 436 Number of extensions: 23 Number of successful extensions: 9 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: 444 Length adjustment: 31 Effective length of query: 358 Effective length of database: 413 Effective search space: 147854 Effective search space used: 147854 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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