Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate GFF2666 Psest_2719 acetylornithine and succinylornithine aminotransferases/succinylornithine transaminase family
Query= BRENDA::Q9SR86 (481 letters) >FitnessBrowser__psRCH2:GFF2666 Length = 406 Score = 171 bits (434), Expect = 3e-47 Identities = 121/396 (30%), Positives = 191/396 (48%), Gaps = 36/396 (9%) Query: 94 VFDENGRRYLDAFGGIATVSCGHCHPEVVNSVVKQLKLINHSTILYLNHTISDFAEALVS 153 V+D++GR +D GGIA + GH HP +V ++ +Q + H + +Y N A+ LV+ Sbjct: 36 VWDQSGRELVDFAGGIAVNALGHAHPAMVAALTEQAGKLWHISNIYTNEPALRLAKKLVA 95 Query: 154 TLPGDLKVVFFTNSGTEANELAMMMARLYTGCN------DIVSLRNSYHGNAAATMGATA 207 D FF NSG EANE A +AR Y +I+S NS+HG T+ Sbjct: 96 ATFADR--AFFCNSGAEANEAAFKLARRYAHDVYGPQKFEIISALNSFHGRTLFTVTVGG 153 Query: 208 QSNWK--FNVVQSGVHHAINPDPYRGIFGSDGEKYASDVHDLIQFGTSGQVAGFIGESIQ 265 QS + F G+ H PY + + ++ S + + E IQ Sbjct: 154 QSKYSDGFGPKIEGITHV----PYNDL-------------EALKAAISDKTCAVVLEPIQ 196 Query: 266 GVGGIVELAPGYLPAAYDIVRKAGGVCIADEVQSGFARTGTHFWGFQSHGVIPDIVTMAK 325 G GI+ YL A + + + I DEVQ+G RTG F + +G+ PDI+T AK Sbjct: 197 GESGILPGEQAYLEGARQLCNEHNALLIFDEVQTGMGRTGELF-AYMHYGITPDILTNAK 255 Query: 326 GIGNGIPLGAVVTTPEIAGVLSRRSYFNTFGGNPMCTAAGHAVLRVLHEEKLQENANLVG 385 +G G P+GA++TT EIA LS ++ T+GGNP+ A AV+ +++ ++ E Sbjct: 256 SLGGGFPIGAMLTTNEIAAHLSVGTHGTTYGGNPLACAVAEAVVDIVNTPEVLEGVKAKH 315 Query: 386 SHLKRRLTLLKNKYELIGDVRGRGLMLGVEFVKDRDLKTPAKAETLHLMDQMKEMGVLVG 445 K RLT + +Y + VRGRGL++G L K + ++ ++V Sbjct: 316 ERFKARLTQIGERYGVFSLVRGRGLLIGCV------LSDAWKGKAGAFCAAAEKEALMVL 369 Query: 446 KGGFYGNVFRITPPLCFTLSDADFLVDVMDHAMSKM 481 + G +V R+ P L +D D +D ++ A++ + Sbjct: 370 QAG--PDVVRLAPSLVIDQADIDEGLDRLERAVAAL 403 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: 451 Number of extensions: 21 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: 481 Length of database: 406 Length adjustment: 32 Effective length of query: 449 Effective length of database: 374 Effective search space: 167926 Effective search space used: 167926 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