Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate GFF3809 PS417_19505 2,4-diaminobutyrate 4-aminotransferase
Query= BRENDA::Q9SR86 (481 letters) >FitnessBrowser__WCS417:GFF3809 Length = 464 Score = 195 bits (495), Expect = 3e-54 Identities = 144/436 (33%), Positives = 218/436 (50%), Gaps = 22/436 (5%) Query: 64 IIAKRREFLSPALFHFYNTPLNIVEAKMQYVFDENGRRYLDAFGGIATVSCGHCHPEVVN 123 ++A++R+ S A + PL + AK YV D GRR++D G T++ GH HP V+ Sbjct: 25 LLARQRQQESNARSYPRRIPLALKRAKGLYVEDVEGRRFIDCLAGAGTLALGHNHPVVIE 84 Query: 124 SVVKQLKLINHSTILYLNHTISD-FAEALVSTLPGDL----KVVFFTNSGTEANELAMMM 178 ++ + L L L + D F + L LP L K+ F +GT+A E A+ + Sbjct: 85 AIQQVLADELPLHTLDLTTPVKDQFVQDLFGLLPPALAREAKIQFCGPTGTDAVEAALKL 144 Query: 179 ARLYTGCNDIVSLRNSYHG---NAAATMGATAQSNWKFNVVQSGVHHAINPDPYRGIFGS 235 R TG + ++S + YHG A + MG+ ++ +GV P YR FG Sbjct: 145 VRTATGRSTVLSFQGGYHGMSQGALSLMGSLGPKKPLGALLGNGVQFLPYPYDYRCPFGL 204 Query: 236 DG-EKYASDVH---DLIQFGTSGQV--AGFIGESIQGVGGIVELAPGYLPAAYDIVRKAG 289 G E ++H +L+ +G + A I E +QG GG++ +L I +AG Sbjct: 205 GGAEGVRVNLHYLDNLLNDPEAGVLLPAAVIVEVVQGEGGVIPADLDWLRGLRRITEQAG 264 Query: 290 GVCIADEVQSGFARTGTHFWGFQSHGVIPDIVTMAKGIGNGIPLGAVVTTPEIAGVLSRR 349 I DE+QSGF RTG F F+ G+IPD+V M+K IG +PL VV + L Sbjct: 265 VALIVDEIQSGFGRTGKLF-AFEHAGIIPDVVVMSKAIGGSLPLAVVVYRDWLDTWLPG- 322 Query: 350 SYFNTFGGNPMCTAAGHAVLRVLHEEKLQENANLVGSHLKRRLTLLKNKYELIGDVRGRG 409 ++ TF GN M AAG AV+R L + L +A +G L L +L+ + +GD+RGRG Sbjct: 323 AHAGTFRGNQMAMAAGSAVMRYLKDHDLAGHAAAMGERLGEHLRILQRDFPHLGDIRGRG 382 Query: 410 LMLGVEFVK-----DRDLKTPAKAETLHLMD-QMKEMGVLVGKGGFYGNVFRITPPLCFT 463 LMLGVE V D P + L+ + + G+++ GG +G+V R PPL T Sbjct: 383 LMLGVELVDPNGTLDVQGHPPVHRQLAPLVQRECLKRGLILELGGRHGSVVRFLPPLVIT 442 Query: 464 LSDADFLVDVMDHAMS 479 + D + D+ A++ Sbjct: 443 AVEVDLVADIFGRALA 458 Lambda K H 0.320 0.136 0.406 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: 594 Number of extensions: 37 Number of successful extensions: 6 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: 481 Length of database: 464 Length adjustment: 33 Effective length of query: 448 Effective length of database: 431 Effective search space: 193088 Effective search space used: 193088 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: 51 (24.3 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