Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_083800327.1 DESAC_RS12075 pyridoxal phosphate-dependent aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >NCBI__GCF_000195295.1:WP_083800327.1 Length = 373 Score = 226 bits (575), Expect = 1e-63 Identities = 136/373 (36%), Positives = 207/373 (55%), Gaps = 19/373 (5%) Query: 27 AQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGHHGYVLSNGILECRQAVTRKIKKLYNK 86 AQG +++ G+G+PDF+TP+++ +AA KA+ +G Y + G+L ++A+ K K+ + Sbjct: 3 AQGIDIVNFGIGEPDFETPENIKEAAIKAIRDGFTRYTPAGGVLALKEAIVEKFKRDNDL 62 Query: 87 DIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHPTPAFPIYESMINYTGSTPVPYDLTED 146 D PE +++ GGK +Y Q E G E+I P+P + Y M+ +TPV E Sbjct: 63 DYRPEEIIVSCGGKHALYNLFQVLFEKGDEVIVPSPYWVSYPPMVMLAEATPVIVPTPEA 122 Query: 147 KDLKFDPEKILSLITDKTRLLILINPNNPTGSFVEKSAIDVLAEGLKKHPHVAILSDEIY 206 K PE + + IT +T+ LIL +P+NPTGS +S + LAE + H + ++SD+IY Sbjct: 123 NGFKLTPEVLRAHITPRTKGLILNSPSNPTGSVYTRSELAALAEVILDH-KLFVVSDDIY 181 Query: 207 SRQIYDGKEMPTFFNY----PDLQDRLIVLDGWSKAYAMTGWRMGWSVWPEELIPHVNKL 262 + ++DG E FFN P+L+ + VL+G SK YAMTGWR+G+ +I V L Sbjct: 182 EKILFDGLE---FFNLAQLDPELKKLVFVLNGVSKTYAMTGWRIGYLAGDARVIKAVTNL 238 Query: 263 IINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQRRKLIHEGLNSLPGVECSLPGGAF 322 S S + +Q A + A++GP DA+ M+ +F RR I + +PG++C PGGAF Sbjct: 239 QSQSTSNPCSIAQKAALEAINGPQDAVAAMVQEFAWRRDDILTRVARIPGLKCVKPGGAF 298 Query: 323 YAFP---------KVIGTGMNGSEFAKKCMHEAGVAIVPGTAFGKTCQDYVRFSYAASQD 373 Y FP K G G A + EA VA+V G FG+ +RFSYA S++ Sbjct: 299 YVFPNFSYYYNKIKPDGQGSYSDPLADFLLEEAHVALVAGIGFGEDA--CLRFSYATSRE 356 Query: 374 NISNALENIKKML 386 I+ L I+ L Sbjct: 357 RIATGLARIEAAL 369 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: 408 Number of extensions: 19 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: 373 Length adjustment: 30 Effective length of query: 357 Effective length of database: 343 Effective search space: 122451 Effective search space used: 122451 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