Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate GFF3586 Psest_3653 4-aminobutyrate aminotransferase, prokaryotic type
Query= curated2:Q5JFW3 (362 letters) >FitnessBrowser__psRCH2:GFF3586 Length = 426 Score = 175 bits (443), Expect = 2e-48 Identities = 126/378 (33%), Positives = 195/378 (51%), Gaps = 48/378 (12%) Query: 18 VWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIV-VAGPMFEHDEREEMLEELS 76 V D +GR ++D GI V GH HP+ + + QL K+ + ++ E+ E+++ Sbjct: 36 VVDVEGREFIDFAGGIAVLNTGHLHPKIIKAVEDQLHKLTHTCFQVLAYEPYVELCEKIN 95 Query: 77 HWVDYEYV---YMGNSGTEAVEAAIKFARLATGRSEIVAMTNAFHGRTLGSLSATWK-KK 132 V ++ + +G+EAVE A+K AR ATGR+ ++A T A+HGRT+ +L T K Sbjct: 96 ARVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVAP 155 Query: 133 YREGFGPLVPG----------FKHIPFNNVEAAKEAITK------ETAAVIFEPIQGEGG 176 Y G G L+PG + ++ A+ E I K + AA+I EP+QGEGG Sbjct: 156 YSAGMG-LMPGGIFRALYPCAIYGVSVDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGG 214 Query: 177 IVPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNG 235 A ++F+ LR L ++ G LLIADEVQ+G RTG F A+E GV D+ T K +G G Sbjct: 215 FNVAPKDFMARLRALCDEHGILLIADEVQTGAGRTGTFFAMEQMGVVADLTTFAKSVGGG 274 Query: 236 FPVSLTLTDLE----IPRGKHGSTFGGNPLACRAVATTLRILRRDRLVEK---------A 282 FP++ E I G G T+ GNPL+C A L + ++L+++ Sbjct: 275 FPIAGVCGKAEIMDAIAPGGLGGTYAGNPLSCAAALAVLEVFEEEKLLDRCKAVAERLTT 334 Query: 283 GEKFMEFSGERVVKTRGRGLMIGIVL------RRPA----GNYVKALQERGILVNTAGN- 331 G K ++ + + + RG G MI I L RPA V +++G+++ + G Sbjct: 335 GLKAIQTKHKEIGEVRGLGAMIAIELFEDGDHARPAAALTSQIVARARDKGLILLSCGTY 394 Query: 332 -RVIRLLPPLIIEGDTLE 348 V+R+L PL E + L+ Sbjct: 395 YNVLRVLVPLTAEDELLD 412 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: 352 Number of extensions: 17 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: 426 Length adjustment: 31 Effective length of query: 331 Effective length of database: 395 Effective search space: 130745 Effective search space used: 130745 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