Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_013644315.1 METBO_RS03630 pyridoxal phosphate-dependent aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >NCBI__GCF_000191585.1:WP_013644315.1 Length = 372 Score = 223 bits (569), Expect = 5e-63 Identities = 124/366 (33%), Positives = 209/366 (57%), Gaps = 12/366 (3%) Query: 19 LAEAKKL-EAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGHHGYVLSNGILECRQAVT 77 L+E +++ E G+ I LGLG+PDFKTPQ+++DAA +A++EG Y + GI+E R+A+ Sbjct: 16 LSEIRRMFEIAGENAISLGLGEPDFKTPQNIIDAATQAMNEGFTHYTSNMGIIELREAIA 75 Query: 78 RKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHPTPAFPIYESMINYTGST 137 K++K + V++ G +Y +Q PG E++ P P F Y + Sbjct: 76 DKLEKENGISSSADSVIVTVGASEAVYVCMQALINPGDEVLIPDPGFLSYSACAKLADGV 135 Query: 138 PVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFVEKSAIDVLAEGLKKHPH 197 PV + E+ DL+ + +L IT KT+ +IL +P+NP GS ++K + +AE + Sbjct: 136 PVGIKIKEENDLRMTCDDVLESITPKTKAIILNSPSNPIGSVMKKKDVKGIAE-IADDND 194 Query: 198 VAILSDEIYSRQIYDGKEMPTFFNYPDLQDRLIVLDGWSKAYAMTGWRMGWSVWPEELIP 257 + I+SDE+Y + IYD K ++ + I ++ +SK YAMTG+R+G+ + + Sbjct: 195 IYIISDEVYEKIIYDSKH----YSAGQFSENAITINAFSKTYAMTGFRIGYISANDSIAE 250 Query: 258 HVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQRRKLIHEGLNSLPGVECSL 317 + K+ +C ++ +Q A + AL+GP +++ M+ +F +RR LI + L+ + G++C + Sbjct: 251 ELLKVHQYIAACASSMAQKAALEALEGPQNSVKSMVSEFKKRRDLIIKRLSGM-GIDCPV 309 Query: 318 PGGAFYAFPKVIGTGMNGSEFAKKCMHEAGVAIVPGTAFGKTCQDYVRFSYAASQDNISN 377 P GAFY FPKV S+ KK GV +V G AFG+ D+VR SYA + D + Sbjct: 310 PEGAFYVFPKVDNPEKFVSDGLKK-----GVVMVNGKAFGEQGSDHVRLSYATAYDKLEE 364 Query: 378 ALENIK 383 A++ ++ Sbjct: 365 AMDRLE 370 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: 343 Number of extensions: 22 Number of successful extensions: 5 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: 372 Length adjustment: 30 Effective length of query: 357 Effective length of database: 342 Effective search space: 122094 Effective search space used: 122094 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