Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate CCNA_01446 CCNA_01446 LL-diaminopimelate aminotransferase
Query= BRENDA::D2Z0I0 (402 letters) >FitnessBrowser__Caulo:CCNA_01446 Length = 406 Score = 413 bits (1061), Expect = e-120 Identities = 204/399 (51%), Positives = 273/399 (68%), Gaps = 9/399 (2%) Query: 7 FPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHG 66 F ++++LP YVF VN++K +LR EG DI+D GMGNPD+P QHI+DKL E A P Sbjct: 5 FHRIRRLPPYVFEEVNKIKARLRAEGTDIIDFGMGNPDMPTPQHIVDKLIETARDPKAGR 64 Query: 67 YSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPN 126 YSASKG+P LRKA+ ++Y RR+GV+L+P+ I T+G+KEG+++L A+ PGD +I PN Sbjct: 65 YSASKGVPGLRKAMANYYGRRFGVKLNPDTEVIATLGSKEGFANLAQALTGPGDVIICPN 124 Query: 127 PTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTT 186 P YPIH + I+ GG VP L PE +L + +K S P ++LS+P NPT Sbjct: 125 PAYPIHAFGFIMAGGIIRHVPALS----PEEYLSNISRAVKHSVPPPSVLILSYPSNPTA 180 Query: 187 LCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKG 246 VDL+F+++ V LAK+ + ++ D AY ++ FD PPSILQV+GA D+AVE+ S+SK Sbjct: 181 QWVDLDFYKDAVALAKKHDLLVISDVAYGEIYFDNNPPPSILQVDGAKDIAVEVNSLSKT 240 Query: 247 FSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRR 306 ++MAGWRV VVGN + LA +KSYLDYG +TP+QVA+ AL P + V++ R IY+ Sbjct: 241 YAMAGWRVGMVVGNARICAALARVKSYLDYGAYTPVQVAAATALNGPQDCVDEIRGIYKS 300 Query: 307 RRDVLVEGLNRVGWEVKKPKGSMFVWAKVPE---EVGMNSLDFSLFLLREAKVAVSPGIG 363 RRD L++ + GW++ P SMF WAK+PE E G S+ FS L+ EA VAV+PGIG Sbjct: 301 RRDTLIKSMKAAGWDIPNPPASMFAWAKIPEAYREAG--SMLFSRLLIEEAGVAVAPGIG 358 Query: 364 FGEYGEGYVRFALVENEHRIRQAVRGIKKALDKIKSYLA 402 FGEYGEGYVR LVENEHRIRQA R +KK + S LA Sbjct: 359 FGEYGEGYVRIGLVENEHRIRQAARNVKKFIANADSILA 397 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: 533 Number of extensions: 18 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: 406 Length adjustment: 31 Effective length of query: 371 Effective length of database: 375 Effective search space: 139125 Effective search space used: 139125 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