Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate BWI76_RS20495 BWI76_RS20495 alanine transaminase
Query= BRENDA::D2Z0I0 (402 letters) >FitnessBrowser__Koxy:BWI76_RS20495 Length = 412 Score = 453 bits (1165), Expect = e-132 Identities = 222/391 (56%), Positives = 286/391 (73%), Gaps = 5/391 (1%) Query: 2 SEEWMFPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANR 61 S E F ++ +LP YVF + ELK RR GEDI+D MGNPD HI++KLC VA R Sbjct: 5 SPERRFTRIDRLPPYVFNITAELKMAARRRGEDIIDFSMGNPDGATPPHIVEKLCTVAQR 64 Query: 62 PNVHGYSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDT 121 P+ HGYS S+GIPRLR+AI +Y+ RY VE+DPE AI+TIG+KEG +HLMLA L+ GDT Sbjct: 65 PDTHGYSTSRGIPRLRRAISRWYQERYNVEIDPESEAIVTIGSKEGLAHLMLATLDHGDT 124 Query: 122 VIVPNPTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFP 181 V+VPNP+YPIH Y +I G SVP++ DF L I+ S+ KPK ++L FP Sbjct: 125 VLVPNPSYPIHIYGAVIAGAQVRSVPLVEGVDF----FNELERAIRESYPKPKMMILGFP 180 Query: 182 HNPTTLCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELY 241 NPT CV+LEFF++VV LAK+ + +VHD AYAD+ +DG+ PSI+QV GA DVAVE + Sbjct: 181 SNPTAQCVELEFFEKVVALAKRYDVLVVHDLAYADIVYDGWKAPSIMQVPGARDVAVEFF 240 Query: 242 SMSKGFSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNR 301 ++SK ++MAGWR+ F+VGN+ L+ LA +KSY DYG FTP+QVA+I ALE + V Sbjct: 241 TLSKSYNMAGWRIGFMVGNKTLVNALARIKSYHDYGTFTPLQVAAIAALEGDQQCVRDIA 300 Query: 302 EIYRRRRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEE-VGMNSLDFSLFLLREAKVAVSP 360 E Y+RRRDVLV+GL+ GW V+ PK SM+VWAK+PE+ M SL+F+ LL++AKV VSP Sbjct: 301 EQYKRRRDVLVKGLHEAGWMVECPKASMYVWAKIPEQYAAMGSLEFAKKLLQDAKVCVSP 360 Query: 361 GIGFGEYGEGYVRFALVENEHRIRQAVRGIK 391 GIGFG+YG+ +VRFAL+EN RIRQAVRGIK Sbjct: 361 GIGFGDYGDTHVRFALIENRDRIRQAVRGIK 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: 548 Number of extensions: 29 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: 412 Length adjustment: 31 Effective length of query: 371 Effective length of database: 381 Effective search space: 141351 Effective search space used: 141351 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