Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_092344193.1 BLU87_RS01675 acetylornithine transaminase
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_900107645.1:WP_092344193.1 Length = 397 Score = 243 bits (620), Expect = 6e-69 Identities = 133/369 (36%), Positives = 209/369 (56%), Gaps = 20/369 (5%) Query: 13 GEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDEREEML 72 G+G ++ D G+RYLD +AG+ VN LGH HP+ V + Q K++ + ++ E+ Sbjct: 29 GKGCWLTDIDGKRYLDFLAGVAVNSLGHCHPKVVAALQEQAAKLLHCSNYYHIPQQIELA 88 Query: 73 EELSHWVDYEYVYMGNSGTEAVEAAIKFAR------LATGRSEIVAMTNAFHGRTLGSLS 126 E L + V+ NSG EA EAA+K R T R EI+ ++FHGRTL ++S Sbjct: 89 EILCEHSFGDRVFFCNSGAEANEAALKLVRKYSADTYGTDRFEIITAIDSFHGRTLATIS 148 Query: 127 ATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIVPADEEFVK 186 AT + + + GF PL+ GFK++PF ++ A K AI +T A++ EPIQGEGGI + +++ Sbjct: 149 ATGQDRIQSGFAPLISGFKYVPFGDIAALKTAIGPKTCAIMMEPIQGEGGINVPPQGYLQ 208 Query: 187 TLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLTLT-- 243 R+L + LLI DE+Q GL RTGK A EH V PD++T+ K + G P+ + Sbjct: 209 AARELCDKHNLLLIFDEIQVGLGRTGKLFAYEHDNVEPDVMTLAKALAAGPPIGAMIARE 268 Query: 244 --DLEIPRGKHGSTFGGNPLACRAVATTLRILRRDRLVE---------KAGEKFMEFSGE 292 + G HGSTFGGNPL A +++L D +++ KA + ++ Sbjct: 269 KYATALSPGTHGSTFGGNPLLTAAGVAAMKVLLEDHIIDNCVAMGNYLKAQLEQLQNKYT 328 Query: 293 RVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIEGDTLEEARK 352 + RGRGL++G+ L VK +RG+L+N +V+R +PPLI+ D +++ + Sbjct: 329 FIKNIRGRGLILGMELTFEGAEIVKTALQRGLLINCTAGKVLRFVPPLIVTQDEIDQMIE 388 Query: 353 EIEGVLNDI 361 ++G+L ++ Sbjct: 389 ILDGILKEL 397 Lambda K H 0.320 0.140 0.410 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: 348 Number of extensions: 18 Number of successful extensions: 5 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: 362 Length of database: 397 Length adjustment: 30 Effective length of query: 332 Effective length of database: 367 Effective search space: 121844 Effective search space used: 121844 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 10 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