Align Aminotransferase class V domain-containing protein (characterized, see rationale)
to candidate WP_026090172.1 C792_RS0101225 alanine--glyoxylate aminotransferase family protein
Query= uniprot:Q2FXK2 (386 letters) >NCBI__GCF_000330705.1:WP_026090172.1 Length = 382 Score = 395 bits (1015), Expect = e-114 Identities = 195/379 (51%), Positives = 272/379 (71%), Gaps = 2/379 (0%) Query: 5 QPLLLTPGPTPVPDAIMREIQAPMVGHRSKDFEDIAQQAFQGLKPIFGSQNDVLILTSSG 64 Q LLLTPGPTP+P + + M+GHRS DF + + GLK I G++N V IL+SSG Sbjct: 3 QKLLLTPGPTPIPPEVSSRMAEGMIGHRSNDFNKLMENIQPGLKAILGTKNPVAILSSSG 62 Query: 65 TSVLEASMLNIVNPEDHFVVIVSGAFGNRFKQIAQTYYKNVHIYDVTWGEAVDVKDFINF 124 TS LE +M+N+V P++ V+IVSG+FG+RF+ IA+TY VH+YDV WG+A D F F Sbjct: 63 TSALETAMVNLVRPDESIVIIVSGSFGDRFRNIAKTYPFEVHVYDVEWGQAADPGRFKEF 122 Query: 125 LSTLNVEVKAVFSQYCETSTTVLHPIHELGNAINQFNSNIYFVVDGVSCIGAVDVDINKD 184 L T VKAVFSQ CETST V+HP++ELG A+ ++S F+VDGVS +G + D+ +D Sbjct: 123 LDTKE-NVKAVFSQSCETSTAVIHPLNELGEAVKSYSSETLFIVDGVSIVGGMTFDMEQD 181 Query: 185 KIDVLVSGSQKAIMLPPGLAFVAYSHRAKEHFKEVTTPKFYLDLNKYISSQADNSTPFTP 244 ID LV+GSQKA+MLPPGLAFVA + A++ + P+FYLD+N+Y + ++STPFTP Sbjct: 182 NIDCLVTGSQKALMLPPGLAFVAMNDTARQKASDNDLPRFYLDINRYFKALEEHSTPFTP 241 Query: 245 NVSLFRGVNAYVETVKAEGFNHVIARHYAIRNALRSALKALDLTLLVNDKDASPTVTAFK 304 VSL +G+ +ET + EG +V RH +R+ LR+ L+ALDLT+LV D+ ASPTVTAF+ Sbjct: 242 AVSLIQGLEKVLETYREEGIENVFERHRNMRDMLRAGLRALDLTMLVADEHASPTVTAFQ 301 Query: 305 PNTNDEVKIIKDELKNRFKITIAGGQGHLKGQILRIGHMGKISPFDILSVVSALEIILTE 364 ++ DE+K+IK++LK+ +ITIAGGQ LKG+ILRIGHMG + P D++ V++A+E ILT+ Sbjct: 302 -SSEDELKVIKNKLKSEHQITIAGGQKDLKGKILRIGHMGYMFPHDMIRVLTAIEAILTD 360 Query: 365 HRKVNYIGKGISKYMEVIH 383 +R NY G+ ++ E + Sbjct: 361 YRNENYYGRAVAAAQEAYY 379 Lambda K H 0.320 0.136 0.392 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: 392 Number of extensions: 10 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: 386 Length of database: 382 Length adjustment: 30 Effective length of query: 356 Effective length of database: 352 Effective search space: 125312 Effective search space used: 125312 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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