Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate 16484 b2379 hypothetical protein (NCBI)
Query= BRENDA::D2Z0I0 (402 letters) >FitnessBrowser__Keio:16484 Length = 412 Score = 451 bits (1159), Expect = e-131 Identities = 221/389 (56%), Positives = 283/389 (72%), Gaps = 5/389 (1%) Query: 4 EWMFPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPN 63 E F ++ +LP YVF + ELK RR GEDI+D MGNPD HI++KLC VA RP+ Sbjct: 7 ERRFTRIDRLPPYVFNITAELKMAARRRGEDIIDFSMGNPDGATPPHIVEKLCTVAQRPD 66 Query: 64 VHGYSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVI 123 HGYS S+GIPRLR+AI +Y+ RY VE+DPE AI+TIG+KEG +HLMLA L+ GDTV+ Sbjct: 67 THGYSTSRGIPRLRRAISRWYQDRYDVEIDPESEAIVTIGSKEGLAHLMLATLDHGDTVL 126 Query: 124 VPNPTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHN 183 VPNP+YPIH Y +I G SVP++ DF L I+ S+ KPK ++L FP N Sbjct: 127 VPNPSYPIHIYGAVIAGAQVRSVPLVEGVDF----FNELERAIRESYPKPKMMILGFPSN 182 Query: 184 PTTLCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSM 243 PT CV+LEFF++VV LAK+ + +VHD AYAD+ +DG+ PSI+QV GA DVAVE +++ Sbjct: 183 PTAQCVELEFFEKVVALAKRYDVLVVHDLAYADIVYDGWKAPSIMQVPGARDVAVEFFTL 242 Query: 244 SKGFSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREI 303 SK ++MAGWR+ F+VGN+ L+ LA +KSY DYG FTP+QVA+I ALE + V E Sbjct: 243 SKSYNMAGWRIGFMVGNKTLVSALARIKSYHDYGTFTPLQVAAIAALEGDQQCVRDIAEQ 302 Query: 304 YRRRRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEE-VGMNSLDFSLFLLREAKVAVSPGI 362 Y+RRRDVLV+GL+ GW V+ PK SM+VWAK+PE M SL+F+ LL EAKV VSPGI Sbjct: 303 YKRRRDVLVKGLHEAGWMVEMPKASMYVWAKIPEPYAAMGSLEFAKKLLNEAKVCVSPGI 362 Query: 363 GFGEYGEGYVRFALVENEHRIRQAVRGIK 391 GFG+YG+ +VRFAL+EN RIRQA+RGIK Sbjct: 363 GFGDYGDTHVRFALIENRDRIRQAIRGIK 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: 549 Number of extensions: 26 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