Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_018125202.1 B149_RS0110945 LL-diaminopimelate aminotransferase
Query= BRENDA::D2Z0I0 (402 letters) >NCBI__GCF_000375485.1:WP_018125202.1 Length = 388 Score = 295 bits (755), Expect = 2e-84 Identities = 157/393 (39%), Positives = 237/393 (60%), Gaps = 7/393 (1%) Query: 1 MSEEWMFPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVAN 60 M E + ++ LP Y+FA +++ K ++ +G DI+ LG+G+PD+P + IID L E A Sbjct: 1 MPEFKLADRLATLPPYLFAAIDKAKAEVAAQGIDIISLGIGDPDLPTPEFIIDALHEGAK 60 Query: 61 RPNVHGYSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGD 120 +P H Y + G+ R A+ D+Y++R+ VELDPE + IG+KEG +H LA + PGD Sbjct: 61 KPVNHQYPSYVGMLEYRTAVADWYRQRFNVELDPESEVVSLIGSKEGIAHFPLAYVNPGD 120 Query: 121 TVIVPNPTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSF 180 V+V P YP++ A GG+ +P+L E D FL L + ++ + K + + + Sbjct: 121 LVLVATPNYPVYPAATGFAGGEVQFLPLLEEND----FLVDLDAVDDDTWARAKMIFVCY 176 Query: 181 PHNPTTLCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPP-SILQVEGALDVAVE 239 P+NPT EF++ +V+ AK+ + +V D AY+++ +D P SIL+VEG DVA+E Sbjct: 177 PNNPTAATATKEFYERLVQKAKEFNVIVVSDLAYSEIYYDPSNKPLSILEVEGGKDVAIE 236 Query: 240 LYSMSKGFSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEK 299 +S+SK ++M GWRVA VGNE LI L +K +D G+F +Q A I AL EK Sbjct: 237 FHSLSKTYNMTGWRVAMAVGNEQLIAGLGKIKENVDSGIFQAVQEAGIAALRHGEPHAEK 296 Query: 300 NREIYRRRRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVGMNSLDFSLFLLREAKVAVS 359 R IY+ RRDV+ + L+ +G + + P+ S +VWAKVPE G S DF +L++ V ++ Sbjct: 297 FRAIYKERRDVVCKALSDIGIQHRVPEASFYVWAKVPE--GNTSADFVTNVLKQTGVVLT 354 Query: 360 PGIGFGEYGEGYVRFALVENEHRIRQAVRGIKK 392 PG GFG GEGY R +L N +++AV I K Sbjct: 355 PGNGFGTPGEGYFRISLTVNNDLLKEAVSRISK 387 Lambda K H 0.322 0.141 0.425 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: 410 Number of extensions: 15 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: 402 Length of database: 388 Length adjustment: 31 Effective length of query: 371 Effective length of database: 357 Effective search space: 132447 Effective search space used: 132447 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 (21.9 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