Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.118 (uncharacterized)
to candidate GFF3586 Psest_3653 4-aminobutyrate aminotransferase, prokaryotic type
Query= curated2:Q9RW75 (429 letters) >FitnessBrowser__psRCH2:GFF3586 Length = 426 Score = 183 bits (464), Expect = 1e-50 Identities = 131/399 (32%), Positives = 196/399 (49%), Gaps = 31/399 (7%) Query: 21 GVYNKHDVVMVRGQGATVWDENGRSYIDCVVGYGVATLGHSHPDVVKAVQEQAGKLM-VM 79 GV H + + ++V D GR +ID G V GH HP ++KAV++Q KL Sbjct: 19 GVGQIHPIFADHAKNSSVVDVEGREFIDFAGGIAVLNTGHLHPKIIKAVEDQLHKLTHTC 78 Query: 80 PQTVPNDKRAEFLQELVGVLPQGL-DRVFLCNSGTEAMEAAKKFAITATGRSRFVSMKRG 138 Q + + E +++ +P + L +G+EA+E A K A ATGR+ ++ Sbjct: 79 FQVLAYEPYVELCEKINARVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGA 138 Query: 139 FSGRSLGALSFTWEPK-------------YREPFGDAVDNKSVDFVTYGNLDEL--RAAV 183 + GR++ L T + +R + A+ SVD + +++ + A Sbjct: 139 YHGRTMMTLGLTGKVAPYSAGMGLMPGGIFRALYPCAIYGVSVDD-SIASIERIFKNDAE 197 Query: 184 TEQTAAVIMEPVQGEGGVRPASAEFIQEARRITREKGALLILDEIQTGFCRTGKMFACEH 243 AA+I+EPVQGEGG A +F+ R + E G LLI DE+QTG RTG FA E Sbjct: 198 PRDIAAIIIEPVQGEGGFNVAPKDFMARLRALCDEHGILLIADEVQTGAGRTGTFFAMEQ 257 Query: 244 FGVIPDGMTLAKAIAGGTPTAAFAMMSEVADRMPAGGHGTTFGGNPLSMAAGVASLRAMK 303 GV+ D T AK++ GG P A +E+ D + GG G T+ GNPLS AA +A L + Sbjct: 258 MGVVADLTTFAKSVGGGFPIAGVCGKAEIMDAIAPGGLGGTYAGNPLSCAAALAVLEVFE 317 Query: 304 REGLAEQAREKGAYMMDKLRAIQS--PKIREVRGLGLMIGVELKEKS---------APYI 352 E L ++ + + L+AIQ+ +I EVRGLG MI +EL E I Sbjct: 318 EEKLLDRCKAVAERLTTGLKAIQTKHKEIGEVRGLGAMIAIELFEDGDHARPAAALTSQI 377 Query: 353 HAMEHDEGVLCLAATPL--VVRFLPPAVISKEQIDQVVA 389 A D+G++ L+ V+R L P E +D+ +A Sbjct: 378 VARARDKGLILLSCGTYYNVLRVLVPLTAEDELLDRGLA 416 Lambda K H 0.317 0.132 0.380 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: 443 Number of extensions: 26 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: 429 Length of database: 426 Length adjustment: 32 Effective length of query: 397 Effective length of database: 394 Effective search space: 156418 Effective search space used: 156418 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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