Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_012169089.1 AZC_RS02835 pyridoxal phosphate-dependent aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >NCBI__GCF_000010525.1:WP_012169089.1 Length = 394 Score = 422 bits (1085), Expect = e-123 Identities = 203/379 (53%), Positives = 273/379 (72%), Gaps = 1/379 (0%) Query: 9 RLGTESAFSVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGHHGYVLSNG 68 R+G E+AF+VLA A L AQG+ +I+LG+GQPDF+TP+H+V+AA KAL +G HGY S G Sbjct: 10 RIGEENAFAVLARATTLAAQGRDIINLGIGQPDFRTPEHIVEAAVKALKDGQHGYTPSVG 69 Query: 69 ILECRQAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHPTPAFPIYE 128 I R+AV R + K ++ ++DP V+IMPGGK TMY AI FGEPGAEI++P P FPIY Sbjct: 70 IQPLREAVARDLHKRFDVEVDPGLVMIMPGGKVTMYAAILLFGEPGAEILYPDPGFPIYR 129 Query: 129 SMINYTGSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFVEKSAIDVL 188 SMI YTG+TP+P + E+ F E+ L+LIT KTRLLI+ +P NPTG K+ ID L Sbjct: 130 SMIEYTGATPIPVPIREENGFAFSAEETLALITPKTRLLIINSPANPTGGVTPKAEIDKL 189 Query: 189 AEGLKKHPHVAILSDEIYSRQIYDGKEMPTFFNYPDLQDRLIVLDGWSKAYAMTGWRMGW 248 +GL HPHVA++SDEIY + ++DG+ T YP+++DRLI+L+GWSK YAMTGWR+G+ Sbjct: 190 VKGLADHPHVALMSDEIYDQFLFDGERHQTLLAYPEIRDRLILLNGWSKTYAMTGWRLGY 249 Query: 249 SVWPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQRRKLIHEGLN 308 S+WP+ L V KL +N+ SCVNA +Q+AGIAAL+GP + + M+ +FD+RR+L+ EGLN Sbjct: 250 SIWPQALYDKVRKLSVNAWSCVNAATQYAGIAALEGPQEPVAAMLAEFDKRRRLVVEGLN 309 Query: 309 SLPGVECSLPGGAFYAFPKVIGTGMNGSE-FAKKCMHEAGVAIVPGTAFGKTCQDYVRFS 367 +LPGV C+ P GAFYAFP V TG ++ A + +AGVA + G FG + Y+R S Sbjct: 310 ALPGVTCAKPKGAFYAFPNVSRTGWTSAKALASALLEDAGVATIGGPDFGVHGEGYIRLS 369 Query: 368 YAASQDNISNALENIKKML 386 YA S +NI+ ALE + L Sbjct: 370 YANSAENIARALERMGAFL 388 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: 486 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: 387 Length of database: 394 Length adjustment: 31 Effective length of query: 356 Effective length of database: 363 Effective search space: 129228 Effective search space used: 129228 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