Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_013706969.1 DESAC_RS10110 aspartate aminotransferase
Query= BRENDA::D2Z0I0 (402 letters) >NCBI__GCF_000195295.1:WP_013706969.1 Length = 393 Score = 467 bits (1202), Expect = e-136 Identities = 226/394 (57%), Positives = 290/394 (73%), Gaps = 5/394 (1%) Query: 7 FPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHG 66 FP++++LP+YVFA VN LK + RR GEDI+DLGMGNPD+P QHI+DKL E A + H Sbjct: 4 FPRLQRLPEYVFATVNALKMEARRRGEDIIDLGMGNPDLPTPQHIVDKLIEAAKLGHNHR 63 Query: 67 YSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPN 126 YSAS+GIP+LR+AI +YKRR+ V++DPE AI TIGAKEG SHL+LA PGD V+VPN Sbjct: 64 YSASRGIPKLREAISSWYKRRFAVDIDPETEAIATIGAKEGLSHLVLATTGPGDVVLVPN 123 Query: 127 PTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTT 186 PTYPIH Y+ +I G +S+P+ P+ DF E L + + +PK +++S+PHNPTT Sbjct: 124 PTYPIHAYSVVIAGAGLVSIPLDPDRDFFE----DLVTITRLIRPRPKMLIISYPHNPTT 179 Query: 187 LCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKG 246 + VDLEFF++VV A++ + I+HDFAYADL FD Y PS LQ+ GA +V VEL+S+SK Sbjct: 180 MVVDLEFFRKVVAYAQEYNVLIIHDFAYADLVFDDYVAPSFLQIPGAKEVGVELFSLSKS 239 Query: 247 FSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRR 306 +SM GWR+ FV GN L+ L +KSYLDYGVF PIQ+ASIIAL PY+ V + Y+ Sbjct: 240 YSMPGWRLGFVCGNPRLVHALTRIKSYLDYGVFQPIQIASIIALNGPYDCVREIVATYQE 299 Query: 307 RRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEV-GMNSLDFSLFLLREAKVAVSPGIGFG 365 RRD L GL R+GW V+ PKG+MFVWAK+P+ M S++F L+REAKVAVSPG+GFG Sbjct: 300 RRDALCRGLQRIGWRVEPPKGTMFVWAKIPKRFREMGSVEFCKMLIREAKVAVSPGLGFG 359 Query: 366 EYGEGYVRFALVENEHRIRQAVRGIKKALDKIKS 399 EYG+ YVRFALVEN HR QA+RG K+ L K+ Sbjct: 360 EYGDEYVRFALVENVHRTNQAIRGFKQVLQGKKT 393 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: 515 Number of extensions: 20 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: 393 Length adjustment: 31 Effective length of query: 371 Effective length of database: 362 Effective search space: 134302 Effective search space used: 134302 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