Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate Synpcc7942_1794 Synpcc7942_1794 succinyldiaminopimelate transaminase
Query= BRENDA::D2Z0I0 (402 letters) >FitnessBrowser__SynE:Synpcc7942_1794 Length = 392 Score = 281 bits (718), Expect = 3e-80 Identities = 141/386 (36%), Positives = 219/386 (56%), Gaps = 4/386 (1%) Query: 9 KVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHGYS 68 ++ L + VFA ++ K G +++DL +G+ D+P H++ + P+ HGY Sbjct: 9 RLAPLQRNVFADMDRAKAVAIAAGREVIDLSLGSSDLPAPDHVVAVIAASLQDPSTHGYL 68 Query: 69 ASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPNPT 128 +G R+ +Y+R++G+ +DPE ++ IG++EG +HL LA++EPG+ ++ +P Sbjct: 69 LHQGTLPFRQVAAAWYERKFGLGVDPETEVLLLIGSQEGTAHLPLAVMEPGEIALLQDPG 128 Query: 129 YPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTTLC 188 YP H + GG+ +P + F F +++ S + +VLS+PHNPTT Sbjct: 129 YPSHAGGVYLAGGEIYRLPTTADRGFLPDFSTIPTEILSRS----RLLVLSYPHNPTTAI 184 Query: 189 VDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKGFS 248 L FF+E V + + + HDF Y DLGFDG PSI Q + A+E +S+SK ++ Sbjct: 185 APLAFFEEAVAFCRHHQLVLAHDFPYPDLGFDGVEVPSIFQADRQKQQAIEFFSLSKSYN 244 Query: 249 MAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRRRR 308 M G+RV F +GN LI L LK+ +D+ + I +I AL P VE R+ +R RR Sbjct: 245 MGGFRVGFAIGNAELIGALRRLKAVVDFNQYQGILAGAIAALTGPQACVEATRQRFRDRR 304 Query: 309 DVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVGMNSLDFSLFLLREAKVAVSPGIGFGEYG 368 D+ + L GW + KP +M++WA +PE SL+F L+ E VA SPGIGFG+ G Sbjct: 305 DIFINALAATGWTIPKPVSTMYLWAPLPEPWQTRSLEFCEKLVAETGVAASPGIGFGDCG 364 Query: 369 EGYVRFALVENEHRIRQAVRGIKKAL 394 EG+VRFALV + R+ +A R I + L Sbjct: 365 EGFVRFALVHDRDRLEEAARRITQFL 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: 387 Number of extensions: 21 Number of successful extensions: 2 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: 392 Length adjustment: 31 Effective length of query: 371 Effective length of database: 361 Effective search space: 133931 Effective search space used: 133931 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