Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_029133363.1 A3GO_RS0110520 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q89RB7 (404 letters) >NCBI__GCF_000428045.1:WP_029133363.1 Length = 450 Score = 145 bits (367), Expect = 2e-39 Identities = 122/435 (28%), Positives = 202/435 (46%), Gaps = 58/435 (13%) Query: 13 TRLGAHNYEPIGVVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHR 72 T++ H + P+ + + RGEGVW+ D DGNRY+D +S++ GH +P+I AA+ Q + Sbjct: 20 TQMKDHEWLPM-IPIKRGEGVWLEDFDGNRYIDAVSSWWVNLFGHANPRINAALKAQVDQ 78 Query: 73 LTLTSRA-FHNDQLAPFYEEIAALT--GSHKVLPMNSGAEAVESAIK----SVRKWGYEV 125 L A F ++ E++ ALT G + +++G+ A+E+A+K S R G++ Sbjct: 79 LEHVMLAGFSHEPAIQLAEKLVALTPPGLDRCFYVDNGSSAIEAALKMSYHSWRNQGHKG 138 Query: 126 KGVPDDQAEIIVCADNFHGRTLGIVGFSTDPETRGHFGPFA---------------PG-- 168 K + ++++HG TLG + + + P PG Sbjct: 139 KH------RFVTLSNSYHGETLGALAVGDVSLYKETYEPLLMEVFTAPSPDCFNREPGES 192 Query: 169 ---FRIIPFGDAAALEQAITPNTVAFLVEP-IQGEAGVIIPPAGYFTKVRELCTANNVML 224 + I F + L + A +VEP +Q G+ + Y +RE C + V L Sbjct: 193 WEAYSIRRFAEMETLLAEHSREISAVIVEPLVQCAGGMRMYHPIYLKLLREACDRHQVHL 252 Query: 225 VLDEIQTGLGRTGKLLAEQHEGIEADVTLLGKALAGGFYPVSAVLSNNEVLGT------- 277 + DEI G GRTG L A + I D L K L G+ P+S VL++ + T Sbjct: 253 IADEIAVGFGRTGTLFACEQADITPDFLCLSKGLTAGYLPLSLVLTSEQTYQTFYDNYEN 312 Query: 278 LRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQGARLLEGLKDIRAN-TVREVR 336 L H ++ GNPL CAVA A++ + ++ +IEN + + E + + V EVR Sbjct: 313 LTAFLHSHSYTGNPLGCAVALASLEIFEQDSVIENNQKLAQVMTEATAHLNDHPRVAEVR 372 Query: 337 GRGLMLAVEL---------HP-EAGRARRYCEALQGKGILAKDTHGHTIRIAPPLVITSD 386 G++LA+E+ +P + R R + +G L + G+ PP VIT + Sbjct: 373 QHGMILAIEMVKDKASRTPYPWQERRGLRVYQHALSRGALLRPL-GNVTYFMPPYVITPE 431 Query: 387 EVDWALEQFATTLTQ 401 ++ + AT T+ Sbjct: 432 QI----RELATIATE 442 Lambda K H 0.319 0.136 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: 464 Number of extensions: 32 Number of successful extensions: 4 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: 404 Length of database: 450 Length adjustment: 32 Effective length of query: 372 Effective length of database: 418 Effective search space: 155496 Effective search space used: 155496 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 Jul 25 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