Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_012283547.1 HM1_RS11430 aminotransferase class V-fold PLP-dependent enzyme
Query= metacyc::MONOMER-21143 (387 letters) >NCBI__GCF_000019165.1:WP_012283547.1 Length = 395 Score = 218 bits (555), Expect = 2e-61 Identities = 118/360 (32%), Positives = 203/360 (56%), Gaps = 4/360 (1%) Query: 25 LEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGHHGYVLSNGILECRQAVTRKIKKLY 84 L A K +I LG+G+PDF TP HV ++ AL+ G+ Y + G E R+ +TR I++ Y Sbjct: 27 LVANTKGVISLGVGEPDFVTPWHVRESCFYALERGYTMYTSNFGTPELRKEITRFIQRSY 86 Query: 85 NKDIDP-ERVLIMPGGKPTMYYAIQCFGEPGAEIIHPTPAFPIYESMINYTGSTPVPYDL 143 D DP VL+ G + A++ PG E++ P P++ Y + G V Sbjct: 87 GVDYDPLSEVLVTVGASEAVDLAMRMLLCPGDEVLVPEPSYVSYSPTVTMAGGVAVAVPT 146 Query: 144 TEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFVEKSAIDVLAEGLKKHPHVAILSD 203 D + E + ++ +T++L+L PNNPTG+ + + ++ +A ++ + +L+D Sbjct: 147 YVKDDFQLTVEALEKKVSPRTKMLVLCYPNNPTGAIMTRPELEAIARFAEERDLI-VLAD 205 Query: 204 EIYSRQIYDGKEMPTFFNYPDLQDRLIVLDGWSKAYAMTGWRMGWSVWPEELIPHVNKLI 263 EIY+ Y+ + + F P ++DR ++++G SK++AMTGWR+G+ ++ I + K+ Sbjct: 206 EIYAELTYEEQHV-CFAGLPGMRDRTVLINGLSKSHAMTGWRIGYVCGNKDFIAQMTKIH 264 Query: 264 INSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQRRKLIHEGLNSLPGVECSLPGGAFY 323 ++ C Q A + AL D M+ ++DQRR+ + N + G+ C P GAFY Sbjct: 265 QYTILCAPIMGQMAALEALRNGDLEKSRMVNQYDQRRRFVVARFNQM-GLTCFNPRGAFY 323 Query: 324 AFPKVIGTGMNGSEFAKKCMHEAGVAIVPGTAFGKTCQDYVRFSYAASQDNISNALENIK 383 AFP + TG++ +F ++ + E VA+VPGTAFG + + ++R SYA+S N++ AL+ I+ Sbjct: 324 AFPSITATGLSSDDFCEQLLAEEKVAVVPGTAFGASGEGFIRVSYASSMANLTTALDRIE 383 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: 404 Number of extensions: 23 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: 395 Length adjustment: 31 Effective length of query: 356 Effective length of database: 364 Effective search space: 129584 Effective search space used: 129584 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