Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_012411382.1 NPUN_RS25750 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::D2Z0I0 (402 letters) >NCBI__GCF_000020025.1:WP_012411382.1 Length = 403 Score = 334 bits (857), Expect = 2e-96 Identities = 167/395 (42%), Positives = 253/395 (64%), Gaps = 8/395 (2%) Query: 1 MSEEWMFP--KVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEV 58 MS W+ P +++KLP YVFA ++ELK + R +G D++DLGMGNPD +++ Sbjct: 1 MSLNWIVPAERIQKLPPYVFARLDELKAKAREQGLDLIDLGMGNPDGATPAPVVEAAIAA 60 Query: 59 ANRPNVHGYSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEP 118 P HGY +G R+AI ++Y RRYGV LDP+ A+ +G+KEG +HL +A + P Sbjct: 61 LKDPANHGYPPFEGTASFRRAITNWYHRRYGVVLDPDSEALPLLGSKEGLTHLAIAYVNP 120 Query: 119 GDTVIVPNPTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVL 178 GD V+VP+P YP H+ P I GG S+ + PE D+ + L + D + R+ K + Sbjct: 121 GDLVLVPSPAYPAHFRGPAIAGGKIHSLILKPENDWL-IDLAAIPDEVA---RQAKILYF 176 Query: 179 SFPHNPTTLCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAV 238 ++P NPT EFF+E+V A++ I +VHD YA+L FDGY P S+L++ GA D+ V Sbjct: 177 NYPSNPTAATAPREFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGV 236 Query: 239 ELYSMSKGFSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVE 298 E +++SK ++MAGWRV FVVGN +I+ L LK+ LDYG+F+ +Q A+ AL+ P + Sbjct: 237 EFHTLSKTYNMAGWRVGFVVGNRHVIQGLRTLKTNLDYGIFSALQKAAETALQLPDVYLH 296 Query: 299 KNREIYRRRRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVGMNSLDFSLFLLREAKVAV 358 + ++ YR RRD L++GL +GW++ + K +M++W K P VGM S DF+L +L++ V + Sbjct: 297 EVQQRYRTRRDFLIDGLGELGWDIPRTKATMYLWVKCP--VGMGSTDFALNVLQQTGVVL 354 Query: 359 SPGIGFGEYGEGYVRFALVENEHRIRQAVRGIKKA 393 +PG FG GEGYVR +L+ + R+ +A+ K+A Sbjct: 355 TPGNAFGVAGEGYVRISLIADCDRLGEALHRFKQA 389 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: 465 Number of extensions: 24 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: 403 Length adjustment: 31 Effective length of query: 371 Effective length of database: 372 Effective search space: 138012 Effective search space used: 138012 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 10 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