Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_013258785.1 DEBA_RS09890 pyridoxal phosphate-dependent aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >NCBI__GCF_000143965.1:WP_013258785.1 Length = 397 Score = 221 bits (564), Expect = 2e-62 Identities = 137/396 (34%), Positives = 213/396 (53%), Gaps = 13/396 (3%) Query: 1 MKLAKNLQRLGTESAFSVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGH 60 M+L++ + + ++ A+A ++ A+G +I+ +GQPDF TP+ + AA KA+++G Sbjct: 1 MELSRRVTSIAPSPTLALDAKANQMRAEGIDVINFTVGQPDFNTPERICQAAIKAINDGF 60 Query: 61 HGYVLSNGILECRQAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHP 120 Y + G E +QAV K K+ D P++V+I GGK + Y +Q G E++ P Sbjct: 61 TRYTPAAGTPELKQAVCGKFKRDNGLDYTPDQVMINVGGKHSGYLVMQALLNEGDEVVVP 120 Query: 121 TPAFPIYESMINYTGSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFV 180 P + Y M+ G TPV E K ++ +++KT+ + L +P+NPTG+ Sbjct: 121 APYWVSYPPMVILAGGTPVIVPTQEKNKFKLQLAELEKAVSNKTKAIFLNSPSNPTGAAY 180 Query: 181 EKSAIDVLAEGLKKHPHVAILSDEIYSRQIYDG-KEMPTFFNYPDLQDRLIVLDGWSKAY 239 + +A+ + + I+SDEIY +YDG K T P + + L+G SKAY Sbjct: 181 SAEELLPVAQFCAER-GILIVSDEIYEPMMYDGAKFTATASLSPLIYQNTVTLNGVSKAY 239 Query: 240 AMTGWRMGWSVWPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQR 299 AMTGWR+G+ P +LI +K+ S S + +Q A + AL+GP D + M+ F +R Sbjct: 240 AMTGWRIGYMGGPVDLIKACSKIQSQSTSNPTSIAQKAAVEALNGPQDDVKAMVEVFARR 299 Query: 300 RKLIHEGLNSLPGVECSLPGGAFYAFP--------KVIGTGMNG-SEFAKKCMHEAGVAI 350 R LI++ LN +PGV C P GAFYAFP K M G SE + + A VA+ Sbjct: 300 RDLIYDLLNQIPGVSCFKPEGAFYAFPNFAAYYGKKAGDKVMTGSSELCEHLLATAHVAL 359 Query: 351 VPGTAFGKTCQDYVRFSYAASQDNISNALENIKKML 386 VPG+AFG + +RFS+A S + I +E + L Sbjct: 360 VPGSAFGH--DECIRFSFATSDELIKAGVERVATAL 393 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: 428 Number of extensions: 21 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: 397 Length adjustment: 31 Effective length of query: 356 Effective length of database: 366 Effective search space: 130296 Effective search space used: 130296 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