Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_012609563.1 G491_RS0128560 LL-diaminopimelate aminotransferase
Query= BRENDA::D2Z0I0 (402 letters) >NCBI__GCF_000429905.1:WP_012609563.1 Length = 388 Score = 311 bits (797), Expect = 2e-89 Identities = 156/384 (40%), Positives = 238/384 (61%), Gaps = 7/384 (1%) Query: 9 KVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHGYS 68 ++K+LP Y+FA ++ K ++R +G DI+DLG+G+PD+P HII L E A P H Y Sbjct: 9 RLKQLPPYLFAEIDRKKEEVRAKGVDIIDLGVGDPDLPTPDHIIKALNEAAKDPRYHRYP 68 Query: 69 ASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPNPT 128 + G+ KA+ FY +R+GV L+ I IG+KEG +H+ LA + PGD +VP+P Sbjct: 69 SYSGMGAFNKAVARFYDKRFGVNLELSE-IITLIGSKEGIAHIPLAYINPGDVALVPSPA 127 Query: 129 YPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTTLC 188 YP++ CGG +P+L E F L L + + K K + +++P+NPT Sbjct: 128 YPVYQIGVEFCGGSCHIMPLLKENGF----LPDLDAIPEDVASKAKLMFINYPNNPTAAV 183 Query: 189 VDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKGFS 248 D FF++V++ AK+ I + HD AY ++ FDGY P S ++V+GA +V +E +S+SK ++ Sbjct: 184 ADEAFFKKVIEFAKKYKIIVCHDAAYTEMSFDGYAPMSFMEVDGAKEVGIEFHSLSKTYN 243 Query: 249 MAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRRRR 308 M GWR+ F VGN +I L +KS +D G F +Q+A I AL+ + V N +IY+ RR Sbjct: 244 MTGWRLGFAVGNAEVIGALGKVKSNIDSGAFDAVQMAGIEALDGDQQCVADNSKIYQERR 303 Query: 309 DVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVGMNSLDFSLFLLREAKVAVSPGIGFGEYG 368 D+L+EGLN +G + PK + ++W +VPE G +S DF LL EA + +PG GFG G Sbjct: 304 DLLMEGLNAMGLKCTPPKATFYMWVEVPE--GYSSADFCTKLLTEAGIVATPGNGFGAPG 361 Query: 369 EGYVRFALVENEHRIRQAVRGIKK 392 EGY R AL +N+ R+ +AV+ +++ Sbjct: 362 EGYFRMALTQNKDRMAEAVKRMQE 385 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: 416 Number of extensions: 18 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