Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate PP_0817 PP_0817 aminotransferase
Query= BRENDA::D2Z0I0 (402 letters) >FitnessBrowser__Putida:PP_0817 Length = 402 Score = 444 bits (1141), Expect = e-129 Identities = 215/387 (55%), Positives = 283/387 (73%), Gaps = 5/387 (1%) Query: 7 FPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHG 66 F ++ +LP YVF + ELK RR GEDI+DL MGNPD HI++KL +VA R + HG Sbjct: 10 FARIDRLPPYVFNITAELKMAARRRGEDIIDLSMGNPDGATPPHIVEKLVQVAQREDTHG 69 Query: 67 YSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPN 126 YS S+GIPRLR+AI ++YK RY V++DPE AI+TIG+KEG +HLMLA L+ GDTV+VPN Sbjct: 70 YSTSRGIPRLRRAISNWYKDRYEVDIDPESEAIVTIGSKEGLAHLMLATLDQGDTVLVPN 129 Query: 127 PTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTT 186 P+YPIH Y +I G SVP++P DF L I+ S KPK ++L FP NPT Sbjct: 130 PSYPIHIYGAVIAGAQVRSVPLVPGVDF----FNELERAIRESIPKPKMMILGFPSNPTA 185 Query: 187 LCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKG 246 CV+L+FF+ VV LAKQ + +VHD AYAD+ +DG+ PSI+QV GA D+AVE +++SK Sbjct: 186 QCVELDFFERVVALAKQYNVLVVHDLAYADIVYDGWKAPSIMQVPGAKDIAVEFFTLSKS 245 Query: 247 FSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRR 306 ++MAGWR+ F+VGN L+ LA +KSY DYG FTP+QVA+I ALE + V E YR+ Sbjct: 246 YNMAGWRIGFMVGNPELVSALARIKSYHDYGTFTPLQVAAIAALEGDQQCVRDIAEQYRQ 305 Query: 307 RRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVG-MNSLDFSLFLLREAKVAVSPGIGFG 365 RR++LV+GL+ +GW V+ PK SM+VWAK+P E + SL+FS LL E KV VSPGIGFG Sbjct: 306 RRNLLVKGLHELGWMVENPKASMYVWAKIPPEYAHLGSLEFSKKLLAETKVCVSPGIGFG 365 Query: 366 EYGEGYVRFALVENEHRIRQAVRGIKK 392 +YG+ +VRFAL+EN+ RIRQA+RGI++ Sbjct: 366 DYGDDHVRFALIENQDRIRQAIRGIRQ 392 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: 402 Length adjustment: 31 Effective length of query: 371 Effective length of database: 371 Effective search space: 137641 Effective search space used: 137641 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