Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_012851925.1 TCUR_RS07730 pyridoxal phosphate-dependent aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >NCBI__GCF_000024385.1:WP_012851925.1 Length = 404 Score = 164 bits (416), Expect = 3e-45 Identities = 117/372 (31%), Positives = 189/372 (50%), Gaps = 25/372 (6%) Query: 18 VLAEAKKLEAQGKPMIHLGLGQP---DFKTPQHVVDAAKKALDEGHHGYVLSNGILECRQ 74 VL AK+LEA+G ++ L +G P F+ P ++ + L E H GY S GIL R+ Sbjct: 20 VLKRAKELEAEGHQILKLHIGNPAPFGFEAPPEILQDVIRNLPEAH-GYSDSKGILSARR 78 Query: 75 AVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHPTPAFPIYESMINYT 134 A+ + ++ + +D E V + G + +Q G E++ P P +P++ + + Sbjct: 79 AIVQHYEERGFEGLDVEDVYLGNGVSELITMTLQALLNNGDEVLIPAPDYPLWTASVCLG 138 Query: 135 GSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFVEKSAIDVLAEGLKK 194 G TPV Y E D + + + IT++T+ L++INPNNPTG+ + ++ LAE ++ Sbjct: 139 GGTPVHYLCDEQAGWAPDLDDVEAKITERTKALVIINPNNPTGAVYSRQVLERLAELARR 198 Query: 195 HPHVAILSDEIYSRQIYDGKEMPTFFNY-PDLQDRLIVLDGWSKAYAMTGWRMGWSV--- 250 H + I SDEIY R +YDG E + PDL + G SK Y + G+R GW V Sbjct: 199 H-GLIIFSDEIYDRVLYDGAEHISIATLAPDL--LCLTFGGLSKNYRVAGFRSGWVVLSG 255 Query: 251 ---WPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMV---KFDQRRKLIH 304 E I ++ ++ N C N P+Q A AAL G +I+E+++ + ++R Sbjct: 256 PKEHAESYIEGLD-ILANMRLCPNVPAQHAIQAALGG-HQSINELVLPTGRLGEQRDRAW 313 Query: 305 EGLNSLPGVECSLPGGAFYAFPKV---IGTGMNGSEFAKKCMHEAGVAIVPGTAFGKTCQ 361 + LN +PGV C P GA Y FP++ + + +F + + + + +V GT F Sbjct: 314 KLLNEIPGVSCVKPQGALYVFPRLDPEVYPIKDDMQFVLELLEDQKLLVVQGTGFNWPAH 373 Query: 362 DYVR---FSYAA 370 D+ R YAA Sbjct: 374 DHFRVVTLQYAA 385 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: 414 Number of extensions: 29 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: 404 Length adjustment: 31 Effective length of query: 356 Effective length of database: 373 Effective search space: 132788 Effective search space used: 132788 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 Jul 25 2024. The underlying query database was built on Jul 25 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