Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_027722706.1 H589_RS0114540 LL-diaminopimelate aminotransferase
Query= BRENDA::D2Z0I0 (402 letters) >NCBI__GCF_000425265.1:WP_027722706.1 Length = 388 Score = 294 bits (752), Expect = 3e-84 Identities = 152/394 (38%), Positives = 239/394 (60%), Gaps = 9/394 (2%) Query: 1 MSEEWMFPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVAN 60 M E + ++ LP Y+FA +++LK ++ +G DI+ LG+G+PD+P + II+ L + A Sbjct: 1 MPEFKLADRLATLPPYLFAQIDKLKAEVAAQGVDIISLGIGDPDLPTPEFIIEALYKAAQ 60 Query: 61 RPNVHGYSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGD 120 P H Y + G+ R+A+ D+YK R+ VELD + + IG+KEG +H LA + PGD Sbjct: 61 NPVNHQYPSYVGLLTFRQAVADWYKERFNVELDAKTEVVSLIGSKEGIAHFPLAFVNPGD 120 Query: 121 TVIVPNPTYPIHYYAPIICGGDAISVPILPEEDF-PEVFLRRLYDLIKTSFRKPKAVVLS 179 V+V +P YP++ A GG+ VP+L E DF P++ L + + K K + ++ Sbjct: 121 LVLVASPNYPVYPVASNFAGGEVEFVPLLEENDFLPDLSL-----IDDAKWDKAKVIFVN 175 Query: 180 FPHNPTTLCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFD-GYTPPSILQVEGALDVAV 238 +P+NPT+ EF++E++ AK+ + +V D AY ++ +D P SIL+ GA DVA+ Sbjct: 176 YPNNPTSAVATPEFYEELIAKAKKHNVIVVSDAAYTEVYYDENKKPLSILETPGAKDVAI 235 Query: 239 ELYSMSKGFSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVE 298 E +S+SK ++M GWR VGN L+ L +K +D G+F +Q A I+AL+ V+ Sbjct: 236 EFHSLSKTYNMTGWRCGMAVGNASLVAGLGKIKENVDSGIFQAVQEAGIVALKEGEPYVK 295 Query: 299 KNREIYRRRRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVGMNSLDFSLFLLREAKVAV 358 + R+IY+ RRD ++E L ++ K P+ S+FVWAK P+ G S +F LL+E V V Sbjct: 296 EFRKIYKERRDYVIEALEKINISCKVPEASIFVWAKTPK--GYTSSEFVSKLLKETGVVV 353 Query: 359 SPGIGFGEYGEGYVRFALVENEHRIRQAVRGIKK 392 +PG GFGE GEGY R +L + R+++AV I + Sbjct: 354 TPGNGFGESGEGYFRISLTVDTDRLKEAVSRISQ 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: 400 Number of extensions: 14 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