Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate GFF2092 PGA1_c21250 aspartate aminotransferase AatA
Query= metacyc::MONOMER-21143 (387 letters) >FitnessBrowser__Phaeo:GFF2092 Length = 400 Score = 225 bits (573), Expect = 2e-63 Identities = 130/392 (33%), Positives = 207/392 (52%), Gaps = 13/392 (3%) Query: 3 LAKNLQRLGTESAFSVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGHHG 62 L+ +L R+ + ++ A +L A G+ +I L G+PDF TP ++ +AA +A+ G Sbjct: 4 LSDSLARVKPSPSIAITTLAGELRAAGRDVIGLSAGEPDFDTPDNIKEAAIRAIQAGKTK 63 Query: 63 YVLSNGILECRQAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHPTP 122 Y +GI E +QAV K + + P +V + GGK +Y A+ PG E++ P P Sbjct: 64 YTAPDGIAELKQAVCDKFARDNGLEYTPAQVSVGTGGKQILYNALMATLNPGDEVVIPAP 123 Query: 123 AFPIYESMINYTGSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFVEK 182 + Y M+ G TP+ + + + K P+++ + IT KT+ + +P+NPTG+ Sbjct: 124 YWVSYPDMVRLAGGTPICVESSLETGFKITPDQLEAAITPKTKWFVFNSPSNPTGAGYHP 183 Query: 183 SAIDVLAEGLKKHPHVAILSDEIYSRQIYDGKEMPTFFNY-PDLQDRLIVLDGWSKAYAM 241 + + L + L +HPHV +++D++Y ++D T P L DR + +G SKAYAM Sbjct: 184 NELKALTDVLLRHPHVWVMTDDMYEHLVFDDFTFCTPAQIEPKLYDRTLTCNGVSKAYAM 243 Query: 242 TGWRMGWSVWPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQRRK 301 TGWR+G++ P+ LI + K+ S S SQ+A + AL+G D I F +RR Sbjct: 244 TGWRIGYAAGPKPLIDAMRKIQSQSTSNPCTISQWAAVEALNGTQDYILPNTAVFRRRRD 303 Query: 302 LIHEGLNSLPGVECSLPGGAFYAFPKVIG----TGMNG------SEFAKKCMHEAGVAIV 351 L+ L+ + GV C +P GAFY +P + G T G FAK + EA VA+V Sbjct: 304 LVISMLSQIEGVACPVPDGAFYVYPSIAGLIGRTSAGGVAITDDEAFAKALLEEADVAVV 363 Query: 352 PGTAFGKTCQDYVRFSYAASQDNISNALENIK 383 G A+G R SYAA+ + ++ A I+ Sbjct: 364 HGAAYG--LSPNFRISYAAADETLTEACRRIQ 393 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: 423 Number of extensions: 26 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: 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 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