Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate N515DRAFT_3630 N515DRAFT_3630 4-aminobutyrate aminotransferase
Query= curated2:Q97GH9 (387 letters) >FitnessBrowser__Dyella79:N515DRAFT_3630 Length = 469 Score = 153 bits (386), Expect = 1e-41 Identities = 113/428 (26%), Positives = 198/428 (46%), Gaps = 68/428 (15%) Query: 17 FDKGEGTKLYDKDGNEYIDFVSGVAVNCLGHCNPSIVKAIEEQSSKLMHVSNYYWNENAM 76 F G+G+ +YD G ++D + G+ N + ++ Q L V++ Y ++ + Sbjct: 41 FRHGQGSWMYDTAGVPFLDLQMWYSAVNFGYGNKRLNDTLKAQIDTLPQVASQYLHQTRI 100 Query: 77 ELTEILCKNSEFD-----KVFMCNSGTEAIEAGLKLARKYALLHGDENKKEIIY-MDNSF 130 EL + + +++ +V G +A+E LKL R Y +N K +++ + + Sbjct: 101 ELAKTIAVDAQQKFGLKGRVHFNVGGAQAVEDSLKLVRNY------KNGKSLMFAFEGGY 154 Query: 131 HGRTMGALSVTGQPKYQESFKPL-------------------------------IGAVKS 159 HGRT+GA S+T +Y+ F + Sbjct: 155 HGRTLGASSITSSYRYRRRFGHFGERAMFIPFPYPFRRPKGMTPEEYSDACVRQFERLFE 214 Query: 160 VKFNDLDDIKQKISSKTAAVIVEPIQGEGGIIPAKKEYLKLLRDLCDENNALLIFDEVQC 219 ++N + D K ++ AA VEPIQG GG + K + K L+ + D+ L++ DE+Q Sbjct: 215 TEYNGVWDPKVN-QAEYAAFYVEPIQGTGGYVIPPKNFFKDLKKVLDKYGILMVVDEIQM 273 Query: 220 GMGRVGSLFAYQKFEVVPDIVCIAKALGGGF-PIGAMLAKESVASS--FVPGDHGNTYGG 276 G R G L++ + F V PDI+ KAL G P+ + A+E + + F PG +T+ Sbjct: 274 GFWRTGKLWSIEHFGVTPDIIVFGKALTNGLNPLSGLWAREEMINPEIFPPGSTHSTFNS 333 Query: 277 NPLACAVAIAVLKELVDKKVVEINVNEKSKYLFDKLMTLKEKYKVINDVRGMGLLIGVEV 336 NPL ++ + V+K + + E NV +K + D L L++++K I DV G+GL + E+ Sbjct: 334 NPLGTSLGLEVIK-MGYELDYETNVAKKGAHFLDALKDLQKRHKEIGDVDGLGLALRAEI 392 Query: 337 ACDVKKIINKCFESKL-----------------LLITAG---KNVVRFLPPLNVSFEEID 376 D NK ++ L++ G KNV+ F P L+++ EEID Sbjct: 393 CTDDGFTPNKALLDRMVDIGLAGDLEHNGKKIGLVLDVGGWYKNVITFAPSLDITHEEID 452 Query: 377 KALGIFEE 384 A+ + ++ Sbjct: 453 LAIALLDQ 460 Lambda K H 0.318 0.137 0.395 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: 393 Number of extensions: 20 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 387 Length of database: 469 Length adjustment: 32 Effective length of query: 355 Effective length of database: 437 Effective search space: 155135 Effective search space used: 155135 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: 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