Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_012050345.1 SWIT_RS21085 4-aminobutyrate--2-oxoglutarate transaminase
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000016765.1:WP_012050345.1 Length = 434 Score = 206 bits (523), Expect = 1e-57 Identities = 146/400 (36%), Positives = 203/400 (50%), Gaps = 51/400 (12%) Query: 12 RGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIV-----VAGPMFEHD 66 R E +WD +GRRY+D +GI V +GH HP + + QL + V G +E Sbjct: 34 RAENAEIWDVEGRRYIDFASGIAVLNVGHRHPRIIAAVEEQLGRFTHTAFQVVG--YEPY 91 Query: 67 ER-EEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARLATGRSEIVAMTNAFHGRTLGSL 125 R E L L+ V +G EA E A+K AR A+GRS ++A N FHGRTL + Sbjct: 92 VRLAERLNALAPVVGPAKTIFFTTGAEATENAVKIARYASGRSAVIAFVNGFHGRTLLAS 151 Query: 126 SATWKK-KYREGFGPLVPGFKHIPFNN------VEAAKEAITK---------ETAAVIFE 169 + T K Y++GFGPL HIPF + VE + A+ AA+I E Sbjct: 152 AMTGKVLPYKKGFGPLPGDIYHIPFPSEAHGITVEHSLAALANVLSSDVEAANVAAIILE 211 Query: 170 PIQGEGGIVPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTM 228 P+QGEGG A EF++ LR L ++ G LIADEVQ+G+ RTGK A+EH GVRPD++T+ Sbjct: 212 PVQGEGGFHVAPFEFLRALRSLCDEHGIALIADEVQTGIGRTGKLFAVEHAGVRPDLITV 271 Query: 229 GKGIGNGFPVSLTLTDL----EIPRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKA-- 282 K +G GFP+S + + +P G G T+ G+P+AC A L ++ +DRL ++A Sbjct: 272 AKSLGGGFPLSAVVGNAALIDRVPPGGLGGTYAGSPIACAAGLAVLDVIEQDRLCDRAER 331 Query: 283 -----GEKFMEFSGER---VVKTRGRGLMIGIVLR------RPAGNYVKAL----QERGI 324 E+ + R + RG G MI +R RP G K + E G+ Sbjct: 332 MGRRITERLSAVAARRELPIGLPRGLGAMIAFDIRAGLDDLRPDGAAAKRVCVRALELGL 391 Query: 325 LVNTAG--NRVIRLLPPLIIEGDTLEEARKEIEGVLNDIL 362 ++ T G IRLL PL L+E + L D L Sbjct: 392 ILLTCGQHGEAIRLLAPLTASDAVLDEGLDILAQALADTL 431 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: 387 Number of extensions: 15 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: 434 Length adjustment: 31 Effective length of query: 331 Effective length of database: 403 Effective search space: 133393 Effective search space used: 133393 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 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