Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_011764553.1 AZO_RS04130 pyridoxal phosphate-dependent aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >NCBI__GCF_000061505.1:WP_011764553.1 Length = 396 Score = 171 bits (433), Expect = 3e-47 Identities = 120/395 (30%), Positives = 193/395 (48%), Gaps = 21/395 (5%) Query: 7 LQRLGTESA-------FSVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEG 59 L RL SA +L A+ LEA G+ +IH+ +G+PDF TP VV AA + LD G Sbjct: 6 LPRLSQRSADVQPFHVMELLRRARDLEAMGRDIIHMEVGEPDFPTPAPVVAAATRFLDGG 65 Query: 60 HHGYVLSNGILECRQAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIH 119 Y + G+ R+A+ R + D+ P+R+++ G + A+ PG E + Sbjct: 66 DVHYTPALGLPALREAIARFYHDRFGADVAPDRIIVTAGASGALMLALAATTNPGDEWLL 125 Query: 120 PTPAFPIYESMI-NYTGSTPVPYDLTEDKDLKFDP--EKILSLITDKTRLLILINPNNPT 176 P P +P ++ ++ G V L D ++ P ++ + + +T L++ P+NPT Sbjct: 126 PDPGYPSNRHLVRSFEG---VAQALPVDAATRYQPTAAQVDAAWSARTLGLMVATPSNPT 182 Query: 177 GSFVEKSAIDVLAEGLKKHPHVAILSDEIYSRQIYDGKEMPTFFNYPDLQ--DRLIVLDG 234 G+ ++ + + L G + + I+ DEIY Y G E T + P L D L V++ Sbjct: 183 GTLLDAAELAALHRGTQARGGLLIV-DEIYQGLTY-GVEASTVLSQPALNAADDLFVVNS 240 Query: 235 WSKAYAMTGWRMGWSVWPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPD--DAIHEM 292 +SK + MTGWR+GW V P + + KL + + P+Q A +AA PD + + Sbjct: 241 FSKYFGMTGWRLGWLVAPPAYVREIEKLAQHFFIAPSTPAQHAALAAF-APDTTEILEAR 299 Query: 293 MVKFDQRRKLIHEGLNSLPGVECSLPGGAFYAFPKVIGTGMNGSEFAKKCMHEAGVAIVP 352 +F RR + L L V + P GAFY + V + + A++ + EAGVA P Sbjct: 300 RHEFAARRDTLLPALRELGFVVATEPQGAFYIYADVSALASDSEQLARRLIEEAGVAATP 359 Query: 353 GTAFG-KTCQDYVRFSYAASQDNISNALENIKKML 386 G FG + ++R +Y QD + A E I +L Sbjct: 360 GLDFGHHHPRRHLRIAYTTRQDRLLEAAERIAAVL 394 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: 380 Number of extensions: 18 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: 396 Length adjustment: 31 Effective length of query: 356 Effective length of database: 365 Effective search space: 129940 Effective search space used: 129940 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