Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_026329666.1 F612_RS0106445 pyridoxal phosphate-dependent aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >NCBI__GCF_000381085.1:WP_026329666.1 Length = 393 Score = 218 bits (554), Expect = 3e-61 Identities = 128/389 (32%), Positives = 209/389 (53%), Gaps = 14/389 (3%) Query: 3 LAKNLQRLGTESAFSVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGHHG 62 L+ + R+ + A+A +L+ GK +I LG G+PDF TPQH+ A A+ G Sbjct: 4 LSDRVNRVKPSLTLVITAKAAELKRAGKDIISLGAGEPDFDTPQHIKAAGITAIQNGQTR 63 Query: 63 YVLSNGILECRQAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHPTP 122 Y +G E ++A+ K K+ + ++L+ GGK + + Q G E+I P P Sbjct: 64 YTAVDGTPELKEAIQAKFKRDNGLEYAMNQILVSSGGKQSFFNLCQAILNDGDEVIIPAP 123 Query: 123 AFPIYESMINYTGSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFVEK 182 + Y M G PV + ++ K ++ IT KT+++++ +P+NPTG+ Sbjct: 124 YWVSYPDMALLAGGEPVIIEAGIEQGFKITATQLEEAITPKTKIMVVNSPSNPTGAVYTA 183 Query: 183 SAIDVLAEGLKKHPHVAILSDEIYSRQIYDGKEMPTFFNY----PDLQDRLIVLDGWSKA 238 + LA+ L K+P++ I SD++Y + +MP F N P+L +R +V++G SKA Sbjct: 184 DELKSLADVLVKYPNIIIASDDMYEHIMI--SDMP-FTNILEVCPELTERTVVMNGVSKA 240 Query: 239 YAMTGWRMGWSVWPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQ 298 Y+MTGWR+G++ P E+I + K+ S S + SQ A +AAL+G + I M+V+F + Sbjct: 241 YSMTGWRIGYAAGPAEIITGMRKVQSQSTSNPCSISQAAAVAALNGSQECIQTMLVEFKK 300 Query: 299 RRKLIHEGLNSLPGVECSLPGGAFYAFPKV-----IGTGMNGSEFAKKCMHEAGVAIVPG 353 R + E +N +PG +C GAFYAF V + ++ + E VA+VPG Sbjct: 301 RHTFVVERINQIPGFKCIEAHGAFYAFMDVSQALTMKNMATDTDLTTALLEEKLVAVVPG 360 Query: 354 TAFGKTCQDYVRFSYAASQDNISNALENI 382 +AFG ++R S+A S +N+ NAL+ I Sbjct: 361 SAFG--ADKHLRISFATSMENLVNALDRI 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: 378 Number of extensions: 20 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: 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