Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_004303932.1 C665_RS07050 pyridoxal phosphate-dependent aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >NCBI__GCF_000310185.1:WP_004303932.1 Length = 400 Score = 166 bits (420), Expect = 1e-45 Identities = 115/374 (30%), Positives = 186/374 (49%), Gaps = 10/374 (2%) Query: 18 VLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGHHGYVLSNGILECRQAVT 77 +L A++LEAQG+ +IH+ +G+PDF TP VV+AA + L G Y + G+ R+A+ Sbjct: 27 LLRRARELEAQGRDIIHMEVGEPDFGTPAPVVEAATRFLAGGDVHYTPALGLPALREAIA 86 Query: 78 RKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHPTPAFPIYESMINYTGST 137 R + D+ PER+++ G + A+ +PG E + P P +P +I Sbjct: 87 RFYHDRFGADVAPERIVVTAGASGALMLALAATTDPGDEWLLPDPGYPSNRHLIR--AFE 144 Query: 138 PVPYDLTEDKDLKFD--PEKILSLITDKTRLLILINPNNPTGSFVEKSAIDVLAEGLKKH 195 V L D ++ PE++ + ++TR L++ P+NPTG+ + + I L + Sbjct: 145 GVARALAVDAASRYQPRPEQVDAAWGERTRGLMVATPSNPTGTLLSVAEIAALHRRTRAR 204 Query: 196 PHVAILSDEIYSRQIYDGKEMPTFFNYPDLQ--DRLIVLDGWSKAYAMTGWRMGWSVWPE 253 V +L DEIY Y G E + P L D + V++ +SK + MTGWR+GW V P Sbjct: 205 GGV-LLVDEIYQGLTY-GVESASALGDPVLNAADDVFVVNSFSKYFGMTGWRLGWLVAPA 262 Query: 254 ELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAI-HEMMVKFDQRRKLIHEGLNSLPG 312 + + KL + + P+Q A +AA AI E +F QRR ++ L +L Sbjct: 263 GFVRELEKLAQHFFISPSTPAQHAALAAFAPATIAILEERRHEFAQRRDVLLPALRALGF 322 Query: 313 VECSLPGGAFYAFPKVIGTGMNGSEFAKKCMHEAGVAIVPGTAFGKTC-QDYVRFSYAAS 371 + P GAFY + V + A++ + EAGVA PG FG + ++R +Y Sbjct: 323 GIAAEPQGAFYVYADVSALADDSEALARRMIEEAGVAATPGLDFGHHLPRRHLRIAYTTH 382 Query: 372 QDNISNALENIKKM 385 + A E I+++ Sbjct: 383 GARLLEAAERIRRL 396 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: 378 Number of extensions: 23 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: 400 Length adjustment: 31 Effective length of query: 356 Effective length of database: 369 Effective search space: 131364 Effective search space used: 131364 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