Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_018123199.1 B149_RS0100510 pyridoxal phosphate-dependent aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >NCBI__GCF_000375485.1:WP_018123199.1 Length = 388 Score = 216 bits (549), Expect = 1e-60 Identities = 121/393 (30%), Positives = 206/393 (52%), Gaps = 15/393 (3%) Query: 1 MKLAKNLQRLGTESAFSVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGH 60 M +++ + ++ VL +A+++E +G ++HL +G+PDF TP + AA ALD+GH Sbjct: 1 MPVSERIAQMKPFMVMEVLEKAQRMEREGASVVHLEIGEPDFDTPASIKRAACAALDDGH 60 Query: 61 HGYVLSNGILECRQAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHP 120 Y S GI E R+A++ ++ Y ++DP R++I G P M+ G E+I Sbjct: 61 THYTHSLGIRELREAISDDYRQRYGVEVDPGRIIITQGTSPAMFVLFSAILRQGQEVIAS 120 Query: 121 TPAFPIYESMINYTGSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFV 180 P + Y + I + G P +TE ++ + ++D+TR L++ +P NPTG+ + Sbjct: 121 NPCYACYHNFIRFAGGEVNPVPVTEQDGWQYRVSAVREAVSDRTRALLINSPANPTGTLL 180 Query: 181 EKSAIDVLAEGLKKHPHVAILSDEIYSRQIYDGKEMPTFFNYPDLQDRLIVLDGWSKAYA 240 + LAE L + ++SDEIY +Y+G+E + D V +G+SK YA Sbjct: 181 SSERMKALAE-LADEKGLHLVSDEIYHGLVYEGREHSVL----EFSDDAFVFNGFSKLYA 235 Query: 241 MTGWRMGWSVWPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQRR 300 MTGWR+G+ + PE + + N N+ +Q+AG+AAL + + M +D RR Sbjct: 236 MTGWRLGYLIAPESFVRPLQIACQNFFISANSMAQWAGVAALREAGEDVEHMKAVYDDRR 295 Query: 301 KLIHEGLNSLPGVECSLPG---GAFYAFP--KVIGTGMNGS--EFAKKCMHEAGVAIVPG 353 + + L+ L G+ S+P GAFY + +GS + A + +A + + PG Sbjct: 296 RYM---LSRLEGMGLSIPNPPTGAFYILVDFRKYAERFDGSSLKLAYDILEKAAIGVTPG 352 Query: 354 TAFGKTCQDYVRFSYAASQDNISNALENIKKML 386 FG + Y+RFSYA S +NI ++ +++ L Sbjct: 353 VDFGPGAEGYIRFSYANSLENIREGMDRLERYL 385 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: 386 Number of extensions: 18 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: 388 Length adjustment: 30 Effective length of query: 357 Effective length of database: 358 Effective search space: 127806 Effective search space used: 127806 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