Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_022949042.1 H035_RS0111080 acetylornithine transaminase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000421465.1:WP_022949042.1 Length = 389 Score = 318 bits (816), Expect = 1e-91 Identities = 174/380 (45%), Positives = 239/380 (62%), Gaps = 7/380 (1%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 +MPTYAR + F RGEG +L+ T G+R+LD +G+AV LGHA+P L AL Q+ +LWH Sbjct: 5 IMPTYARLPVAFSRGEGIWLWDTQGKRYLDAISGIAVCNLGHAHPTLARALCDQSQRLWH 64 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 TSNL+R+ QE+LA+ LT + + VFF NSGAEA E K+ R Y + +G R++ Sbjct: 65 TSNLYRIEPQEALAETLTRLSGMENVFFCNSGAEANEAALKIARAYGHLQGIDT-PRVVV 123 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETA---GICLE 181 +Q+FHGRTLA +SA ++ +GF PLL GF VPFGD AV AV ++ + + +E Sbjct: 124 ADQSFHGRTLATLSATGNPRIQQGFEPLLPGFLRVPFGDPNAV--AVLEDRSDVVAVLVE 181 Query: 182 PIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAV 241 PIQGEGG+R +L LR +CD +G LL LDE+Q G+GRTG+ F + +TPDVM + Sbjct: 182 PIQGEGGVRMPPNGYLAELRRLCDRNGWLLMLDEVQTGIGRTGRWFGGQHEAVTPDVMTL 241 Query: 242 AKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQR 301 AK +G GFP+GACLA KAA +TAG HGST+GGN L V VL + + G +D R Sbjct: 242 AKSLGNGFPIGACLAKGKAAEVLTAGRHGSTFGGNFLGCRVALEVLRIIEQEGLIDRAAR 301 Query: 302 IGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVV 361 +G L++ LA + +P V K +RG+GL+L + +V GLL NV+ Sbjct: 302 LGDQLKEALAHRLGRHPQV-KNIRGRGLILAIELDHPCAHLVPEALERGLLINVTATNVL 360 Query: 362 RLLPPLNIGEAEVEEAVAIL 381 RLLPPL + ++ E+ V L Sbjct: 361 RLLPPLILENSQAEQLVDTL 380 Lambda K H 0.321 0.139 0.414 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: 417 Number of extensions: 17 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: 389 Length of database: 389 Length adjustment: 30 Effective length of query: 359 Effective length of database: 359 Effective search space: 128881 Effective search space used: 128881 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: 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