Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate Dsui_2909 Dsui_2909 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::D2Z0I0 (402 letters) >FitnessBrowser__PS:Dsui_2909 Length = 395 Score = 455 bits (1171), Expect = e-133 Identities = 223/391 (57%), Positives = 285/391 (72%), Gaps = 5/391 (1%) Query: 7 FPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHG 66 FP++K+LP YVF + ELK RR GEDI+D+ MGNPD +HI+DK+ + R + HG Sbjct: 4 FPRIKRLPPYVFNITGELKMAARRRGEDIIDMSMGNPDGATPKHIVDKMVDATQRGDTHG 63 Query: 67 YSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPN 126 YS SKGIPRLRKAICD+Y RRY VE DP+ A++TIG+KEG +HLMLA L+ GDTV+VPN Sbjct: 64 YSVSKGIPRLRKAICDWYLRRYNVEFDPDSEAVVTIGSKEGLAHLMLATLDRGDTVLVPN 123 Query: 127 PTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTT 186 P+YPIH Y II G + SV + + DF E R I+ KPK ++L FP NPT Sbjct: 124 PSYPIHIYGAIIAGANTRSVRMTDDVDFFEELQRA----IRECTPKPKMMILGFPSNPTA 179 Query: 187 LCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKG 246 CV+L+FF+ VV LAK+ I +VHD AYAD+ FDGY PSI++V GA DVAVE ++MSK Sbjct: 180 RCVELDFFERVVALAKEHDILVVHDLAYADIVFDGYRAPSIMEVPGARDVAVEFFTMSKS 239 Query: 247 FSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRR 306 ++MAGWRV ++VGN+ L LA +KSY DYG FTPIQVAS+IAL+ P + VE+ R+ Y Sbjct: 240 YNMAGWRVGYMVGNKELCAALARIKSYHDYGTFTPIQVASVIALDGPQDCVEEVRQTYEL 299 Query: 307 RRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVG-MNSLDFSLFLLREAKVAVSPGIGFG 365 RR+VL +GL+ GW V+ PK SM++WAK+PE + SL+F+ LL EAKVAVSPGIGFG Sbjct: 300 RRNVLAKGLHEAGWMVEVPKASMYIWAKIPEPYAHLGSLEFAKKLLAEAKVAVSPGIGFG 359 Query: 366 EYGEGYVRFALVENEHRIRQAVRGIKKALDK 396 +YG+ +VRFAL+ENE R RQA+RGIK K Sbjct: 360 DYGDDHVRFALIENEARTRQAIRGIKDMFRK 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: 544 Number of extensions: 19 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: 395 Length adjustment: 31 Effective length of query: 371 Effective length of database: 364 Effective search space: 135044 Effective search space used: 135044 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 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