Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_012991079.1 THAL_RS00165 pyridoxal phosphate-dependent aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >NCBI__GCF_000025605.1:WP_012991079.1 Length = 393 Score = 202 bits (513), Expect = 2e-56 Identities = 122/389 (31%), Positives = 201/389 (51%), Gaps = 8/389 (2%) Query: 3 LAKNLQRLGTESAFSVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGHHG 62 L++ ++ + ++ A +L+AQG +I G G+PDF TP + +A KAL EG Sbjct: 2 LSERVKHIKPAPTLALTARVNQLKAQGVDIIGFGAGEPDFDTPDFIKEACIKALREGKTK 61 Query: 63 YVLSNGILECRQAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHPTP 122 Y S GIL R+A++ K+KK + P ++++ G K +Y G E++ P+P Sbjct: 62 YTPSAGILPLREALSEKLKKENRVEYSPSQIVVTAGAKMALYLVFLAVLNEGDEVLLPSP 121 Query: 123 AFPIYESMINYTGSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFVEK 182 + Y I G PV L+EDK E +L IT++TR+L+L +P+NPTG+ V Sbjct: 122 YWVSYPEQIQLCGGKPVVVPLSEDKGFVLTAEDLLPYITERTRMLVLNSPSNPTGAVVPP 181 Query: 183 SAIDVLAEGLKKHPHVAILSDEIYSRQIYDGKEMPTFFNYPDLQDRLIVLDGWSKAYAMT 242 ++ +A+ L + I+SDE Y +Y+G+ + P+++D ++ +SK ++MT Sbjct: 182 KELERIAQ-LCVERRIFIVSDECYEAFVYEGEFVSVASLSPEVRDITFTVNAFSKTFSMT 240 Query: 243 GWRMGWSVWPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPD--DAIHEMMVKFDQRR 300 GWR+G+ PE + L ++S + +Q+ + AL P + +M F +RR Sbjct: 241 GWRVGYVASPEPFARVIADLNSQTLSNATSFAQYGALEALTNPQARSFVEKMKETFRERR 300 Query: 301 KLIHEGLNSLPGVECSLPGGAFYAFPKV-IGTGMNGSE--FAKKCMHEAGVAIVPGTAFG 357 L+ +P V+ P GAFY FP + + GS+ A + + VA VPG+AFG Sbjct: 301 NTALRLLSQIPHVKVVKPSGAFYIFPNFRYYSSLLGSDLALADYLVEKGRVACVPGSAFG 360 Query: 358 KTCQDYVRFSYAASQDNISNALENIKKML 386 + Y+R SY S I + IK+ L Sbjct: 361 --AEGYLRLSYCLSSQEIEEGIGRIKEAL 387 Lambda K H 0.319 0.137 0.414 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: 370 Number of extensions: 23 Number of successful extensions: 5 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: 387 Length of database: 393 Length adjustment: 31 Effective length of query: 356 Effective length of database: 362 Effective search space: 128872 Effective search space used: 128872 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 (21.7 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