Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_011386083.1 AMB_RS18860 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::D2Z0I0 (402 letters) >NCBI__GCF_000009985.1:WP_011386083.1 Length = 410 Score = 417 bits (1073), Expect = e-121 Identities = 204/395 (51%), Positives = 271/395 (68%), Gaps = 5/395 (1%) Query: 1 MSEEWMFPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVAN 60 MS + F ++K+LP YVFA VN +K + R GEDI+D GMGNPD P HI+DKL E A Sbjct: 1 MSSQHDFHRIKRLPPYVFAEVNAMKARARAAGEDIIDFGMGNPDQPTPAHIVDKLVEAAR 60 Query: 61 RPNVHGYSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGD 120 P H YS S+GIP LRKA+ +Y+RR+ V++DPE I+T+G+KEG ++L A+ PGD Sbjct: 61 NPRAHRYSMSRGIPGLRKALSGYYQRRFAVDIDPETECIVTLGSKEGLANLANAITSPGD 120 Query: 121 TVIVPNPTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSF 180 V+VPNP+YPIH Y II GG VP+ P+ +F L+ L ++ S KP A+VL++ Sbjct: 121 IVLVPNPSYPIHPYGFIIAGGSCRFVPVTPDAEF----LKALDRAVRHSVPKPIALVLNY 176 Query: 181 PHNPTTLCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVEL 240 P NPT L DL+F+ +VV+ + GIWI+ D AY+++ FD PPSILQ+ GA ++AVE Sbjct: 177 PSNPTALLADLDFYGQVVEFCRHHGIWILSDLAYSEIYFDVAPPPSILQIPGAKEIAVEF 236 Query: 241 YSMSKGFSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKN 300 SMSK ++M GWR+ F GN+ LI L +KSYLDYG FTPIQVA+ AL P + V+ Sbjct: 237 TSMSKTYNMPGWRIGFAAGNKTLIAALGRIKSYLDYGAFTPIQVAATAALNGPQDCVDDI 296 Query: 301 REIYRRRRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVG-MNSLDFSLFLLREAKVAVS 359 R +Y+ RRD L+EGL+ GWE+ P +MF WA +P+ + SL+FS L+REA+VAV+ Sbjct: 297 RALYKGRRDALIEGLSAAGWEIPSPPATMFAWAPIPKAFAHLGSLEFSKLLMREAQVAVA 356 Query: 360 PGIGFGEYGEGYVRFALVENEHRIRQAVRGIKKAL 394 PGIGFGEYG+ +VR LVEN R RQAVR IK L Sbjct: 357 PGIGFGEYGDSHVRIGLVENVQRTRQAVRNIKTFL 391 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: 513 Number of extensions: 25 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: 410 Length adjustment: 31 Effective length of query: 371 Effective length of database: 379 Effective search space: 140609 Effective search space used: 140609 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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