Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate Synpcc7942_2545 Synpcc7942_2545 aspartate aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >FitnessBrowser__SynE:Synpcc7942_2545 Length = 392 Score = 246 bits (628), Expect = 8e-70 Identities = 131/384 (34%), Positives = 215/384 (55%), Gaps = 4/384 (1%) Query: 1 MKLAKNLQRLGTESAFSVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGH 60 MKL++ + R+ ++ A+AK ++A+G + G+PDF+TP H+ +AA +AL EG Sbjct: 1 MKLSERVGRVSPSLTLAIAAQAKAMKAEGLDVCSFSAGEPDFETPLHIRNAAAQALAEGK 60 Query: 61 HGYVLSNGILECRQAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHP 120 Y + G + R+A+ +K++ D +L+ GGK ++Y +Q +PG E+I P Sbjct: 61 TRYGPAAGEPDLREAIAQKLRADNGLDYQAANILVTNGGKQSLYNLMQVLLDPGDEVIIP 120 Query: 121 TPAFPIYESMINYTGSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFV 180 P + Y M+ G PV + K P+++ IT +TRLL+L +P+NPTG Sbjct: 121 APYWLSYPEMVKLAGGVPVIVETFASDGFKLQPQQLAGAITPRTRLLVLNSPSNPTGMVY 180 Query: 181 EKSAIDVLAEGLKKHPHVAILSDEIYSRQIYDGKEMPTFFNY-PDLQDRLIVLDGWSKAY 239 + ++ +A ++ H ++SDEIY + +YDG + + + P +R ++ +G++KAY Sbjct: 181 SRQELEAIAPIIEAH-DFWVVSDEIYEKILYDGADHHSIGSLSPACFERTLISNGFAKAY 239 Query: 240 AMTGWRMGWSVWPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQR 299 +MTGWR+G+ P ELI L +S S V +Q+ IAAL GP D + EM+ F +R Sbjct: 240 SMTGWRVGYLAGPSELIAAAASLQSHSTSNVCTFAQYGAIAALQGPQDCVAEMLAAFTER 299 Query: 300 RKLIHEGLNSLPGVECSLPGGAFYAFPKVIGTGMNGSEFAKKCMHEAGVAIVPGTAFGKT 359 R+LI GLN + G+ C +P GAFY F + TG++ + ++ + + VA +PG AFG Sbjct: 300 RQLILNGLNQIAGLSCPIPEGAFYVFVDISKTGLDSMTYCRQLLDQHQVAAIPGIAFGD- 358 Query: 360 CQDYVRFSYAASQDNISNALENIK 383 +R SYA I LE ++ Sbjct: 359 -DRSIRLSYATDCQTIEKGLERLQ 381 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: 366 Number of extensions: 18 Number of successful extensions: 3 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: 392 Length adjustment: 30 Effective length of query: 357 Effective length of database: 362 Effective search space: 129234 Effective search space used: 129234 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 09 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