Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate AO353_28150 AO353_28150 arginine aminotransferase
Query= BRENDA::D2Z0I0 (402 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28150 Length = 667 Score = 173 bits (438), Expect = 2e-47 Identities = 120/381 (31%), Positives = 190/381 (49%), Gaps = 13/381 (3%) Query: 21 VNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHGYSASKGIPRLRKAI 80 ++ + +R GED++ L +G+PD P I D + + H Y+ G LR+AI Sbjct: 20 IHNAAFDAQRRGEDVIILSVGDPDFPTPDFITDAAVDALREGDTH-YTEIAGRLALREAI 78 Query: 81 CDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPNPTYPIHYYAPIICG 140 Y + +G EL N I GA+ L +L GD V+ +P Y + G Sbjct: 79 AARYSQLFGRELQAS-NVINVAGAQNALFITSLCLLTAGDEVLALDPMYVTYEATLKASG 137 Query: 141 GDAISVPILPEEDFPEVFLRRLYD--LIKTSFRKPKAVVLSFPHNPTTLCVDLEFFQEVV 198 + VP + F RL L K + +A+ LS P+NPT + ++ E Q + Sbjct: 138 ATLVRVPCAADSGF------RLDAAVLAKAITPRTRAIFLSNPNNPTGVVLNREELQAIA 191 Query: 199 KLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKGFSMAGWRVAFVV 258 LA +W+V D Y L F+ S+ + G + V + S+SK +M GWR+ ++V Sbjct: 192 DLAITHDLWVVVDEVYESLAFER-EHLSLAALPGMAERCVVIGSLSKSHAMTGWRIGWIV 250 Query: 259 GNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRRRRDVLVEGLNRV 318 +E L+ + L + YG+ + A++ A+++ EV REIYRRRRD++V+GL+ Sbjct: 251 ADETLVAHAETLMLSMLYGLPGFVMEAALKAVQAHEEVTHGMREIYRRRRDLVVKGLSDC 310 Query: 319 -GWEVKKPKGSMFVWAKVPEEVGMNSLDFSLFLLREAKVAVSPGIGFGEYGEGYVRFALV 377 G V P MFV V G++SL+F+ LLREA+V+V FGE +G+VR + Sbjct: 311 PGISVLTPDAGMFVLVDV-RGTGLSSLEFAWRLLREARVSVLDAAAFGEPAQGFVRLSFT 369 Query: 378 ENEHRIRQAVRGIKKALDKIK 398 E R+ QA + I+ + +K Sbjct: 370 LGEERLAQACQRIRDFIQVLK 390 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: 530 Number of extensions: 29 Number of successful extensions: 5 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: 667 Length adjustment: 35 Effective length of query: 367 Effective length of database: 632 Effective search space: 231944 Effective search space used: 231944 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 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