Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_012992556.1 THAL_RS07735 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= BRENDA::Q9BYV1 (514 letters) >NCBI__GCF_000025605.1:WP_012992556.1 Length = 451 Score = 160 bits (404), Expect = 1e-43 Identities = 127/392 (32%), Positives = 189/392 (48%), Gaps = 48/392 (12%) Query: 83 QKPLLLHQGHMEWLFDAEGSRYLDFFSGIVTVSVGHCHPKVNAVAQKQLGRLWHTSTV-F 141 ++ L+ +G +L+D G +++D S + GH HPK+N +QL ++ HT+T+ Sbjct: 28 EENLIFEKGEGVYLYDIYGRKFIDAISSLWCNVHGHNHPKLNRALIEQLQKVAHTTTLGS 87 Query: 142 FHPPMHEYAEKLAALLPEPLKVIFLVNSGSEANELAMLMARAHSNNID-----IISFRGA 196 + P A++L + P L +F G+EA E+A+ MA + N +SFR A Sbjct: 88 SNVPAILLAKRLVDISPPGLTKVFYSEDGAEAVEIAIKMAYHYWRNRGEKRRVFVSFREA 147 Query: 197 YHGCSPYTLGLTNVGTYKMELPGGTGCQPTMCPDVFRGPWGGSHCRDSPVQTIRKCS--- 253 YHG T+G +VG D+F G + RD +TI S Sbjct: 148 YHGD---TVGAVSVGGI----------------DLFHGTY-----RDLLFETIFLPSPYL 183 Query: 254 -CAPD----CCQAKDQYIEQFKDTLSTSVAKSIAGFFAEPIQGVNGVVQYPKGFLKEAFE 308 C C + K++ + +D L +A IQ G++ +PKGFLK E Sbjct: 184 FCKERYGRLCDECKEELLGMLEDVLRRR-DDVVAVVLEAGIQAAAGMLPFPKGFLKGVRE 242 Query: 309 LVRARGGVCIADEVQTGFGRLGSHFWGFQTHDVLPDIVTMAKGIGNGF-PMAAVITTPEI 367 L + G + I DEV TGFGR GS F+ Q DV PD + + KGI G+ P+AA +TT E+ Sbjct: 243 LTKRYGVLMIVDEVATGFGRTGSMFY-CQQEDVSPDFMCLGKGITGGYLPLAATLTTDEV 301 Query: 368 AKSL------AKCLQHFNTFGGNPMACAIGSAVLEVIKEENLQENSQEVGTYMLLKFAKL 421 + K H +T+ GN +ACA+ A LE+ +EE E Q Y+ + + Sbjct: 302 FNAFLGEFGEKKHFYHGHTYTGNNLACAVALANLEIFEEERTLEKLQPKIEYLRERLQSM 361 Query: 422 RDEFEIVGDVRGKGLMIGIEMVQDKISCRPLP 453 E VGDVR G M GIE+V+D+ P P Sbjct: 362 W-ELRHVGDVRQLGFMAGIELVKDRDKGEPFP 392 Lambda K H 0.323 0.138 0.431 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: 530 Number of extensions: 31 Number of successful extensions: 7 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: 514 Length of database: 451 Length adjustment: 34 Effective length of query: 480 Effective length of database: 417 Effective search space: 200160 Effective search space used: 200160 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 52 (24.6 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