Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate 8499593 DvMF_0361 LL-diaminopimelate aminotransferase (RefSeq)
Query= BRENDA::D2Z0I0 (402 letters) >FitnessBrowser__Miya:8499593 Length = 389 Score = 278 bits (710), Expect = 3e-79 Identities = 142/391 (36%), Positives = 233/391 (59%), Gaps = 6/391 (1%) Query: 1 MSEEWMFPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVAN 60 M++ + ++ LP Y+FA ++++K ++ G DI+ LG+G+PD+P II+ + + Sbjct: 1 MADFKLADRLATLPPYLFAGIDKVKAEVAARGVDIISLGIGDPDMPTPDFIIEAMKKAVE 60 Query: 61 RPNVHGYSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGD 120 RP H Y + G+ R+ + ++Y RR+GV LDP+ I IG+KEG +H LA + PGD Sbjct: 61 RPANHQYPSYVGMLEFRQEVANWYGRRFGVSLDPKTEVIGLIGSKEGIAHFPLAFVNPGD 120 Query: 121 TVIVPNPTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSF 180 V+V P YP+++ A GG+ +P++ E D +L L + ++ + K + +++ Sbjct: 121 LVLVCTPNYPVYHIATGFVGGEVQFIPLVEEND----YLPDLDAIPAATWDRAKMIFVNY 176 Query: 181 PHNPTTLCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFD-GYTPPSILQVEGALDVAVE 239 P+NPT F+++++ + ++ + I HD AY ++ +D P SIL+VEGA DV +E Sbjct: 177 PNNPTAATAPRAFYEKLIGICRKHNVIIAHDTAYTEVYYDENDKPMSILEVEGAKDVTIE 236 Query: 240 LYSMSKGFSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEK 299 +S+SK ++M GWRV VGN L+ L +K +D G+F +Q ASI+AL + + Sbjct: 237 FHSLSKTYNMTGWRVGMAVGNASLVAGLGKVKENVDSGIFQAVQEASIVALRDGDDFCRE 296 Query: 300 NREIYRRRRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVGMNSLDFSLFLLREAKVAVS 359 R IYR+RRDV+V LN+VG + P + ++WAKVP G +S +F +L + V ++ Sbjct: 297 LRGIYRKRRDVVVAALNKVGIACRVPTAAFYIWAKVPAGYG-SSAEFVTAVLEKTGVVLT 355 Query: 360 PGIGFGEYGEGYVRFALVENEHRIRQAVRGI 390 PG GFG GEGY R +L + R+ +AV I Sbjct: 356 PGNGFGTPGEGYFRISLTVDTDRLEEAVSRI 386 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: 421 Number of extensions: 17 Number of successful extensions: 4 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: 389 Length adjustment: 31 Effective length of query: 371 Effective length of database: 358 Effective search space: 132818 Effective search space used: 132818 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