Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_005453184.1 SACCYDRAFT_RS02235 pyridoxal phosphate-dependent aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >NCBI__GCF_000244975.1:WP_005453184.1 Length = 410 Score = 246 bits (627), Expect = 1e-69 Identities = 137/398 (34%), Positives = 221/398 (55%), Gaps = 18/398 (4%) Query: 2 KLAKNLQRLGTESAFSVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKAL-DEGH 60 +++ + + + +V A+AK L+A+G+P+I G GQPDF TP+++V+AA A+ D G+ Sbjct: 14 RVSARIAGITPSATLAVDAKAKALKAEGRPVIGFGAGQPDFPTPEYIVEAAAAAVRDRGN 73 Query: 61 HGYVLSNGILECRQAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHP 120 HGY + G+ E R+A+ K + D +VL+ GGK +Y A +PG E++ Sbjct: 74 HGYTAAAGLPELREAIAAKTLRDSGFSCDASQVLVTNGGKQAVYSAFATLLDPGDEVLLL 133 Query: 121 TPAFPIYESMINYTGSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFV 180 P + Y I G PV E + E++ + T++T++L+ +P+NPTG+ Sbjct: 134 APYWTTYPESITLAGGVPVQVTADESTGYRVTVEQLEAARTERTKVLLFNSPSNPTGAVY 193 Query: 181 EKSAIDVLAEGLKKHPHVAILSDEIYSRQIYDGKE---MPTFFNYPDLQDRLIVLDGWSK 237 + ++ + +H + +++DEIY +YDG + +PT P+L DR ++L+G +K Sbjct: 194 TREQVEAIGRWAAEHD-IWVITDEIYEHLVYDGVKAASLPTVV--PELADRTLILNGVAK 250 Query: 238 AYAMTGWRMGWSVWPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFD 297 Y+MTGWR+GW V P+++I + + V SQ A +AA++GP D +HEM FD Sbjct: 251 TYSMTGWRVGWIVGPQDVIKAASSFQSHLCGNVANVSQRAALAAVEGPLDVVHEMRAAFD 310 Query: 298 QRRKLIHEGLNSLPGVECSLPGGAFYAFPK---VIGTGMNGS------EFAKKCMHEAGV 348 RRK I L+ +P VEC P GAFYA+P V+G + G E A + E V Sbjct: 311 SRRKKIVSMLSEIPNVECPTPEGAFYAYPSVKAVLGKEIRGQRPADTVELADLILREVEV 370 Query: 349 AIVPGTAFGKTCQDYVRFSYAASQDNISNALENIKKML 386 A+VPG AFG Y RFSYA ++ ++ + + +L Sbjct: 371 AVVPGEAFG--TPGYFRFSYALAEKDLVEGVTRVADLL 406 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: 27 Number of successful extensions: 6 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: 410 Length adjustment: 31 Effective length of query: 356 Effective length of database: 379 Effective search space: 134924 Effective search space used: 134924 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