Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_092482527.1 BM299_RS05865 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= BRENDA::D2Z0I0 (402 letters) >NCBI__GCF_900115975.1:WP_092482527.1 Length = 390 Score = 318 bits (814), Expect = 2e-91 Identities = 152/386 (39%), Positives = 247/386 (63%), Gaps = 5/386 (1%) Query: 9 KVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHGYS 68 +++ L +F + E+K Q+ ++G ++++LG+G+PD+PP+ HI++ + + P + Y Sbjct: 6 RIQNLSSAIFNEMEEIKKQVEQKGIEVINLGVGSPDLPPAPHIVEAMHRALDNPGNYHYP 65 Query: 69 ASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPNPT 128 G P L +A+ +Y++R+GVELDP+ + +G+++G +H+ +A + PGD +VP+P Sbjct: 66 LV-GKPELHRAVTAWYRKRFGVELDPDNEVLALMGSQDGLAHIAMAYINPGDIALVPDPG 124 Query: 129 YPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTTLC 188 YPI+ + ++ G +P+L + +F L L + + R+ K + +++P+NP Sbjct: 125 YPIYACSILLAEGKIYPMPLLAKNNF----LPDLKAIPEEVARQAKLLWVNYPNNPVAAA 180 Query: 189 VDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKGFS 248 D +FF +V A++ I + HD AY +L FDG+ P S L++ GA +V +E YS+SK ++ Sbjct: 181 ADRDFFTSLVDFAREYDILVCHDIAYCELAFDGFKPISFLEITGAREVGIEFYSLSKTYN 240 Query: 249 MAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRRRR 308 MAG R+ F VGN +++ L +K+ +DYGVF +Q A I ALE P + V +N E YRRRR Sbjct: 241 MAGCRIGFAVGNAEILQGLNRVKTNIDYGVFNVVQEAGIAALEGPQDCVRENAETYRRRR 300 Query: 309 DVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVGMNSLDFSLFLLREAKVAVSPGIGFGEYG 368 DVLV+GL R+GW+V +P+ SMFVWA +PE + +F+L LL + V V PG FGE G Sbjct: 301 DVLVDGLARLGWKVPRPRASMFVWAPLPEGFNCTAREFALQLLHQTGVLVIPGTAFGEQG 360 Query: 369 EGYVRFALVENEHRIRQAVRGIKKAL 394 EGY+R ALV E+ + +AVR I + L Sbjct: 361 EGYLRIALVREENVLARAVRRIGEFL 386 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: 467 Number of extensions: 28 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: 390 Length adjustment: 31 Effective length of query: 371 Effective length of database: 359 Effective search space: 133189 Effective search space used: 133189 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