Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate AZOBR_RS19590 AZOBR_RS19590 ornithine-oxoacid aminotransferase
Query= curated2:Q5JFW3 (362 letters) >FitnessBrowser__azobra:AZOBR_RS19590 Length = 405 Score = 249 bits (637), Expect = 7e-71 Identities = 143/373 (38%), Positives = 211/373 (56%), Gaps = 24/373 (6%) Query: 10 LVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDERE 69 L RGEGVYVWD +G RYLD ++ GH HP+ + M +Q K+ + F +D+ Sbjct: 27 LARGEGVYVWDTEGNRYLDCLSAYSAVNQGHCHPKILEAMVQQASKLTLTSRAFRNDQLA 86 Query: 70 EMLEELSHWVDYEYVYMGNSGTEAVEAAIKFAR--------LATGRSEIVAMTNAFHGRT 121 EEL+ + NSG EAVE+AIK R + ++EI+ ++ FHGRT Sbjct: 87 LFYEELAALTGSHKILPMNSGAEAVESAIKTVRKWGYEVRGVPENQAEIIVCSDNFHGRT 146 Query: 122 LGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIVPAD 181 + +S + R GFGP PGF+ +PF + A + A+T T AV+ EPIQGE G+V Sbjct: 147 ISIVSFSTDPDARGGFGPFTPGFRTVPFGDAAALEAALTPNTVAVLLEPIQGEAGVVIPP 206 Query: 182 EEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGF-PVS 239 +++ +RDL + ++I DE+Q+GL RTGK LA EH GV D+ +GK + GF PVS Sbjct: 207 AGYLRRVRDLCTERNVVMILDEIQTGLGRTGKLLAEEHEGVEADVTLIGKALSGGFYPVS 266 Query: 240 LTLTDLEI----PRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKA---GEKFMEFSG- 291 L++ E+ G+HGSTFGGNPLAC +R+L + +++ A G F+E G Sbjct: 267 AVLSNSEVLGVLKPGQHGSTFGGNPLACAVARAAMRVLVEEGMIDNAAAQGAYFLEQLGA 326 Query: 292 ---ERVVKTRGRGLMIGIVLRRPAG---NYVKALQERGILVNTAGNRVIRLLPPLIIEGD 345 + + RGRGLM+ + L AG Y +AL+ RG+L + IR+ PPL+I + Sbjct: 327 IRSNVIREARGRGLMLAVELHPEAGGARRYCEALRARGVLAKDTHDHTIRIAPPLVITRE 386 Query: 346 TLEEARKEIEGVL 358 ++ A ++ + VL Sbjct: 387 QVDWALEQFDAVL 399 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: 336 Number of extensions: 14 Number of successful extensions: 6 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: 405 Length adjustment: 30 Effective length of query: 332 Effective length of database: 375 Effective search space: 124500 Effective search space used: 124500 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