Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_015944380.1 DHAF_RS15445 diaminopimelate aminotransferase
Query= BRENDA::D2Z0I0 (402 letters) >NCBI__GCF_000021925.1:WP_015944380.1 Length = 388 Score = 305 bits (780), Expect = 2e-87 Identities = 152/386 (39%), Positives = 238/386 (61%), Gaps = 6/386 (1%) Query: 9 KVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHGYS 68 ++ L VF +++L+ +L + G+ +++L +G+PD PS I L E +GY+ Sbjct: 5 RLSSLGASVFTEMDDLRKELEKAGKQLINLSIGSPDRSPSAEIRKVLAEGVLDGGSYGYT 64 Query: 69 ASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPNPT 128 ++G R +YK R+GV LDPE+ + +G+++G +H+ LA+ +PGD ++P+P Sbjct: 65 LTRGTESFRSGCARWYKERFGVNLDPEKEVLPLMGSQDGLAHIFLALCDPGDVALIPDPG 124 Query: 129 YPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTTLC 188 YPI+ ++ GG+ +++P+ E F L L + ++ K + L++P+NPT Sbjct: 125 YPIYTAGLVLAGGEKVALPLREENGF----LPDLSAIEDEVAQQAKIMFLNYPNNPTAAV 180 Query: 189 VDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKGFS 248 L FF+EVV A++ I + HD AY++L FDGY P S LQV GA +V +E +S+SK ++ Sbjct: 181 APLSFFEEVVDFARRNRIVVCHDAAYSELAFDGYRPVSFLQVPGAKEVGIEFHSVSKTYN 240 Query: 249 MAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRRRR 308 +AG R+ F VGN +I LA LKS +DYGVF P A AL + E VE+NR Y+ RR Sbjct: 241 LAGVRLGFAVGNGEIIGALAELKSNIDYGVFEPALQAGAYALSASQENVEQNRRAYQERR 300 Query: 309 DVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVGMNSLDFSLFLLREAKVAVSPGIGFGEYG 368 D+ V+G + GW + P+GSMF+WA VP +S F+ L REA V V PG+ FGEYG Sbjct: 301 DIWVKGCAQAGWSMPSPRGSMFIWAPVP--TAQDSRSFAFALAREAGVIVVPGVAFGEYG 358 Query: 369 EGYVRFALVENEHRIRQAVRGIKKAL 394 EGYVR +V+++ +++AVR +++ L Sbjct: 359 EGYVRIGMVQDQEVLQEAVRRVQEFL 384 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: 405 Number of extensions: 23 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