Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate AZOBR_RS12970 AZOBR_RS12970 aspartate aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >FitnessBrowser__azobra:AZOBR_RS12970 Length = 401 Score = 229 bits (583), Expect = 1e-64 Identities = 133/396 (33%), Positives = 204/396 (51%), Gaps = 13/396 (3%) Query: 3 LAKNLQRLGTESAFSVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGHHG 62 +A L R+ +V +A++L A G+ +I LG G+PDF TP ++ DAA KA+ G Sbjct: 4 IASRLSRIKPSPTIAVTQKARELAAAGRDVIGLGAGEPDFDTPDNIKDAAIKAIQAGDTK 63 Query: 63 YVLSNGILECRQAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHPTP 122 Y +G ++A+ K ++ P+++ + GGK +Y A+ PG E+I P P Sbjct: 64 YTAVDGTPALKKAICAKFERENGLKYAPDQITVGVGGKQVLYNALMATLTPGDEVIIPAP 123 Query: 123 AFPIYESMINYTGSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFVEK 182 + Y M+ TPV ++ K P + IT KT+ LIL +P+NP+G+ + Sbjct: 124 YWVSYPDMVELAEGTPVFVSCPAEQGFKLQPADLEKAITPKTKWLILNSPSNPSGAAYTR 183 Query: 183 SAIDVLAEGLKKHPHVAILSDEIYSRQIYDGKEMPTFFNY-PDLQDRLIVLDGWSKAYAM 241 + L + L KHP V +++D++Y +YDG E T P L DR + ++G SK+YAM Sbjct: 184 DEMKALTDVLVKHPQVWVMTDDMYEHLLYDGIEFVTPAQVEPALYDRTLTVNGVSKSYAM 243 Query: 242 TGWRMGWSVWPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQRRK 301 TGWR+G++ P+ LI + + S S + +Q A + AL+GP D I E F QRR Sbjct: 244 TGWRIGYAGGPKALIKAMGVIQSQSTSNPTSIAQAAAVEALNGPQDFIAERAAVFAQRRD 303 Query: 302 LIHEGLNSLPGVECSLPGGAFYAFPKVIGT----------GMNGSEFAKKCMHEAGVAIV 351 L+ LN G+ C P GAFY +P GT +F + GVA+V Sbjct: 304 LVVSMLNQAKGISCPKPEGAFYVYPSCAGTIGKTTPDGKVIETDEDFVTYLLESEGVAVV 363 Query: 352 PGTAFGKTCQDYVRFSYAASQDNISNALENIKKMLG 387 G+AFG + R SYA S + + A + I++ G Sbjct: 364 QGSAFG--LAPHFRISYATSTEALEEACKRIQRACG 397 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: 429 Number of extensions: 20 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: 401 Length adjustment: 31 Effective length of query: 356 Effective length of database: 370 Effective search space: 131720 Effective search space used: 131720 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