Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate PP_4481 PP_4481 Succinylornithine transaminase/acetylornithine aminotransferase
Query= BRENDA::O30508 (406 letters) >FitnessBrowser__Putida:PP_4481 Length = 406 Score = 672 bits (1734), Expect = 0.0 Identities = 324/406 (79%), Positives = 365/406 (89%) Query: 1 MSAPHAQVERADFDRYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAH 60 MS A V+RADFD+ MVPNY+PAAFIPVRGEGSRVWDQSGRELIDFAGGIAV +LGH H Sbjct: 1 MSVEQAPVQRADFDQVMVPNYSPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVNALGHCH 60 Query: 61 PALVKALTEQAQRIWHVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLAR 120 PALVKALTEQA +WHVSNVFTNEPALRLA KLVDATFA+R F NSGAE+NEAAFKLAR Sbjct: 61 PALVKALTEQANTLWHVSNVFTNEPALRLAHKLVDATFADRAFFCNSGAESNEAAFKLAR 120 Query: 121 RYANDVYGPQKYEIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALK 180 R A+D +GPQK+EIIA NSFHGRTLFTV+VGGQPKYSDGFGPK GI+HVPYNDLEALK Sbjct: 121 RVAHDRFGPQKHEIIATVNSFHGRTLFTVSVGGQPKYSDGFGPKITGISHVPYNDLEALK 180 Query: 181 AAISDKTCAVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFA 240 A ISDKTCAVV+EPIQGE GV+PA +AYLEGARKLCDEHNALL+FDEVQ+G+GR G L+A Sbjct: 181 AQISDKTCAVVIEPIQGESGVVPADKAYLEGARKLCDEHNALLIFDEVQTGVGRTGSLYA 240 Query: 241 YMHYGVVPDILSSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALD 300 Y HYGV+PDIL+SAKSLGGGFPIGAMLTT E+AKHL+VGTHGTTYGGNPL AVA A LD Sbjct: 241 YQHYGVIPDILTSAKSLGGGFPIGAMLTTTELAKHLAVGTHGTTYGGNPLGCAVACAVLD 300 Query: 301 VINTPEVLDGVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNA 360 V+NTPE L G+KAKHERFK+RL++IGQ+Y +F ++RG+GLL+G LT+ WKGKA+DVLNA Sbjct: 301 VVNTPETLAGIKAKHERFKTRLEQIGQQYNLFSQVRGVGLLLGCVLTEAWKGKAKDVLNA 360 Query: 361 AEKEAVMVLQASPDVVRFAPSLVIDDAEIDEGLERFERAVAKLVRG 406 AEKE VMVLQA PDVVRFAPSLV++DA+IDEGL+RFERAVA L +G Sbjct: 361 AEKEGVMVLQAGPDVVRFAPSLVVEDADIDEGLDRFERAVATLTKG 406 Lambda K H 0.318 0.135 0.394 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: 597 Number of extensions: 8 Number of successful extensions: 1 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: 406 Length adjustment: 31 Effective length of query: 375 Effective length of database: 375 Effective search space: 140625 Effective search space used: 140625 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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