Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate Ga0059261_3674 Ga0059261_3674 adenosylmethionine-8-amino-7-oxononanoate transaminase
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >FitnessBrowser__Korea:Ga0059261_3674 Length = 415 Score = 134 bits (336), Expect = 6e-36 Identities = 100/300 (33%), Positives = 146/300 (48%), Gaps = 21/300 (7%) Query: 29 EGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHT-GNGYTNEPVLRLA 87 EG+ L G+ ID V GH +PR+V A+ +QA K G+T+EP +A Sbjct: 26 EGAVLHTADGRRVIDAISSWWVTTHGHGNPRIVAAIRDQAEKLDQLIFAGWTHEPAETVA 85 Query: 88 KQLIDATFA--DRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGRTLFT 145 + L+ D VFF +SG+ + E A+K+A + +R G + I+ + ++HG T+ Sbjct: 86 RDLVAMMPRPLDHVFFSDSGSTSVEVAIKMALGHFANR-GEPRHRIIVMQGSYHGDTIGG 144 Query: 146 VSAGGQPAYSQDFAPLPPQIQHAI-------YNDLDSAKALIDDNT--CAVIVEPMQ-GE 195 +S G + +++ +APL + Y LD+ + L + A+IVEP+ G Sbjct: 145 MSVGARGVFNRSYAPLLFDVDTIPFPEGANEYRALDALEQLCAQSPLPAAMIVEPLVLGA 204 Query: 196 GGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLSTAKAL- 254 GG+ LR +RE+C AH L I DEV TG GRTG L A V PDLL +K L Sbjct: 205 GGMKMYPPGVLRAMREICAAHGVLFIADEVMTGWGRTGTLLACEQAAVVPDLLCLSKGLT 264 Query: 255 GGGFPIGALLA------SERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREVLNGV 308 GG P+ +A S R + H ++Y NP+ACA A A VL V Sbjct: 265 GGSLPLAVTMATPEIFESHRSKDRSKMFFHSSSYTANPIACAAAAANLAIWREEPVLERV 324 Lambda K H 0.321 0.137 0.412 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: 410 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: 406 Length of database: 415 Length adjustment: 31 Effective length of query: 375 Effective length of database: 384 Effective search space: 144000 Effective search space used: 144000 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.
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