Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_010936475.1 DET_RS03860 diaminopimelate aminotransferase
Query= BRENDA::D2Z0I0 (402 letters) >NCBI__GCF_000011905.1:WP_010936475.1 Length = 388 Score = 296 bits (758), Expect = 7e-85 Identities = 138/379 (36%), Positives = 231/379 (60%), Gaps = 6/379 (1%) Query: 9 KVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHGYS 68 +++ LP Y+F +++ + R +GE+++ +G+PD+P +HI+ +LC+ A P H Y Sbjct: 6 RIENLPPYLFVQISKKIAEKRAKGEEVISFAIGDPDLPTPKHILAELCKAAEDPANHRYP 65 Query: 69 ASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPNPT 128 ++G+P LRKA+ ++Y++R+GV+L+P+ + IG+KEG H L+PGD +VP+P Sbjct: 66 ETEGLPVLRKAMAEWYEKRFGVKLNPDTEVLPLIGSKEGIGHAAWCFLDPGDVALVPDPA 125 Query: 129 YPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTTLC 188 YP++ + + G + +P+ E +F F D++ K K + +++P+NPT Sbjct: 126 YPVYAISSQLAGAEVFYMPLNKENNFLPDFNAIPQDVLS----KAKILWINYPNNPTGAV 181 Query: 189 VDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKGFS 248 L+FF+E + A + + + HD Y+++ FDGY P S L+ +GA +V +E +S+SK ++ Sbjct: 182 AGLDFFKEAAEFAAKHNLAVCHDGPYSEIAFDGYRPVSFLEADGAKEVGIEFHSLSKSYN 241 Query: 249 MAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRRRR 308 M GWR+ VGN +I L KS LD G+ IQ+ +I AL +V+ +N +Y+RRR Sbjct: 242 MTGWRIGMAVGNAKMIDALRRFKSNLDSGIPQAIQLMAIAALNGSQDVISQNCAVYQRRR 301 Query: 309 DVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVGMNSLDFSLFLLREAKVAVSPGIGFGEYG 368 D LVE L +G EV PK S+++WA VPE G S F+ LL + V V+PG G+G G Sbjct: 302 DRLVEALRNIGMEVTAPKASLYIWAPVPE--GYTSASFATELLDKTGVVVTPGTGYGTSG 359 Query: 369 EGYVRFALVENEHRIRQAV 387 EGY+R +L + ++ + + Sbjct: 360 EGYIRLSLTVPDEQLEKGI 378 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: 427 Number of extensions: 18 Number of successful extensions: 3 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