Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate Ga0059261_2226 Ga0059261_2226 Aspartate/tyrosine/aromatic aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >FitnessBrowser__Korea:Ga0059261_2226 Length = 399 Score = 199 bits (507), Expect = 9e-56 Identities = 124/395 (31%), Positives = 203/395 (51%), Gaps = 13/395 (3%) Query: 1 MKLAKNLQRLGTESAFSVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGH 60 M+ + L R+ + ++ + +L+ QG +I LG G+PDF TP V +AA +A+ +G Sbjct: 1 MQTSAALNRIQPSATLAMTSRVFELKRQGIDVIGLGAGEPDFDTPDFVKEAAIEAIRKGI 60 Query: 61 HGYVLSNGILECRQAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHP 120 Y +G E + A+ K + ++ + GGK T++ A + G E++ P Sbjct: 61 TKYTNVDGTPELKAAIVGKFARDNGLTYAENQISVNSGGKHTLFNAFCATIDAGDEVVIP 120 Query: 121 TPAFPIYESMINYTGSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFV 180 P + Y ++ + G PV + + K PE++ + IT +T+ ++L +P+NPTG+ Sbjct: 121 APYWVSYPDVVEFAGGKPVFIAAGAEANYKIKPEQLEAAITARTKWVVLNSPSNPTGAAY 180 Query: 181 EKSAIDVLAEGLKKHPHVAILSDEIYSRQIYDGKEMPTFFNY-PDLQDRLIVLDGWSKAY 239 + + L E L++HP+V I +D++Y +YDG E T P L +R + +G SKAY Sbjct: 181 SAAELKALGEVLERHPNVLIYADDMYEHILYDGFEFATIAQVCPSLYERTLTANGVSKAY 240 Query: 240 AMTGWRMGWSVWPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQR 299 AMTGWR+G++ P+ LI + KL S S + SQ A +AAL+G + + F +R Sbjct: 241 AMTGWRIGYAGGPQWLIKAMGKLQSQSTSNPCSVSQAASVAALNGDQSFLKDRAAAFQKR 300 Query: 300 RKLIHEGLNSLPGVECSLPGGAFYAFP-------KVIGTGM---NGSEFAKKCMHEAGVA 349 R L+ L + G+ C P GAFY +P K G+ + +A VA Sbjct: 301 RDLVVSMLGQINGMNCPRPEGAFYVYPEFSQLIGKTTPKGLVIDTDETMVGYLLDDAKVA 360 Query: 350 IVPGTAFGKTCQDYVRFSYAASQDNISNALENIKK 384 V G AFG +R SYA S+D ++ A I++ Sbjct: 361 AVHGGAFG--FSPALRISYATSEDVLAEACGRIQE 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: 413 Number of extensions: 20 Number of successful extensions: 2 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: 399 Length adjustment: 31 Effective length of query: 356 Effective length of database: 368 Effective search space: 131008 Effective search space used: 131008 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