Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_018126051.1 B149_RS0115315 pyridoxal phosphate-dependent aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >NCBI__GCF_000375485.1:WP_018126051.1 Length = 390 Score = 229 bits (583), Expect = 1e-64 Identities = 140/391 (35%), Positives = 209/391 (53%), Gaps = 9/391 (2%) Query: 1 MKLAKNLQRLGTESAFSVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGH 60 M++++ L RL + +V +A++L AQG+ ++ L +GQPDF TP HVV+AAK ALDEG Sbjct: 1 MRISERLSRLKPSATLAVNTKAQELRAQGREIVSLAVGQPDFGTPAHVVEAAKAALDEGF 60 Query: 61 HGYVLSNGILECRQAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHP 120 Y GI E R+AV + Y E +I GGK +Y + PG E++ P Sbjct: 61 TRYTPVPGIPELREAVADYYGRFYGITAVQENAIISNGGKQVLYNLLMALVNPGDEVLVP 120 Query: 121 TPAFPIYESMINYTGSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFV 180 P + Y +MI V + D E + + T++TR+L+L +P+NPTG Sbjct: 121 APYWVSYPAMIELAEGRCVTVPTEAENDFLVSVEGLEAARTERTRVLVLNSPSNPTGCCY 180 Query: 181 EKSAIDVLAEGLKKHPHVAILSDEIYSRQIYDGKEMPTFFNYPDLQDRLIVLDG-WSKAY 239 + +D +A+ + V I+SDE+Y R +Y E T + L G SK++ Sbjct: 181 TQDQLDGIAQWALDN-GVFIISDEVYDRLVYAPVEPATLARFWQKHPESCALVGALSKSF 239 Query: 240 AMTGWRMGWSVWPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQR 299 MTGWR+GW++ EEL+ ++K+ S S V++ SQ AG+ AL G D + +M F +R Sbjct: 240 CMTGWRLGWALAAEELVKAMSKIQGQSTSNVSSFSQKAGVVALAGEWDIVEQMKEAFVRR 299 Query: 300 RKLIHEGLNSLPGVECSLPGGAFYAFPKV----IGTGMNGSEFAKKCMHEAGVAIVPGTA 355 R + HE + S G C P GAFY FP + + + K + EAGVA+VPG+A Sbjct: 300 RDIAHEIITSW-GAPCPKPDGAFYLFPVLDAFYTEDAPDSAAMCNKILEEAGVALVPGSA 358 Query: 356 FGKTCQDYVRFSYAASQDNISNALENIKKML 386 FG +RFSYA D + +AL + K+L Sbjct: 359 FGD--DRCIRFSYAVDDDTLRDALTRVGKVL 387 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: 398 Number of extensions: 21 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: 390 Length adjustment: 30 Effective length of query: 357 Effective length of database: 360 Effective search space: 128520 Effective search space used: 128520 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