Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_086508150.1 BZY95_RS01045 aspartate aminotransferase family protein
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_002151265.1:WP_086508150.1 Length = 404 Score = 521 bits (1341), Expect = e-152 Identities = 247/395 (62%), Positives = 319/395 (80%) Query: 10 RADFDRYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTE 69 RADFD+YMVPNY+P IPVRGEGSR+WDQ GRE IDFAGGIAV SLGH HP LVKALTE Sbjct: 7 RADFDQYMVPNYSPQKVIPVRGEGSRLWDQEGREYIDFAGGIAVNSLGHCHPVLVKALTE 66 Query: 70 QAQRIWHVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGP 129 Q ++WH+SNV+TNEP+L+LA+ LV+ TFA++ + +SG EANEAA KLARR+A+D +G Sbjct: 67 QGNKLWHLSNVYTNEPSLKLAKTLVERTFADKAYFCSSGGEANEAALKLARRWAHDNFGE 126 Query: 130 QKYEIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDKTCA 189 K+ I++ SFHGRT FTV+VGGQPKYS GFGP GI H +N+L++++ I+D TCA Sbjct: 127 HKHRIVSFYQSFHGRTFFTVSVGGQPKYSQGFGPVPGGIVHGEFNNLDSVRDLINDDTCA 186 Query: 190 VVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPD 249 V++EP+QGEGG+ PA Q +L+G R LCD H+ALL+FDEVQ+G+GR G L+AYM YG+ PD Sbjct: 187 VMVEPMQGEGGITPATQEFLQGLRDLCDAHDALLIFDEVQTGVGRTGSLYAYMEYGIEPD 246 Query: 250 ILSSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLD 309 IL+SAK+LGGGFPIGAMLTT +A L++GTHG+TYGGN LASAVA AA++ I+TPEVL Sbjct: 247 ILTSAKALGGGFPIGAMLTTDRVAPALAIGTHGSTYGGNALASAVALAAVEHIDTPEVLG 306 Query: 310 GVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVL 369 GVK +H+ F+ L+ I +++G+F EIRGMGLLIGA +T E+K +A+D+L A +E +M L Sbjct: 307 GVKQRHDLFREHLEAINRKHGVFREIRGMGLLIGAEMTPEYKDRAKDILPLAIEEGLMAL 366 Query: 370 QASPDVVRFAPSLVIDDAEIDEGLERFERAVAKLV 404 A P+V+R APSLVI +A+I EG+ R ERA+ +LV Sbjct: 367 IAGPNVLRMAPSLVIPEADIAEGMARLERAIERLV 401 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: 542 Number of extensions: 17 Number of successful extensions: 2 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: 404 Length adjustment: 31 Effective length of query: 375 Effective length of database: 373 Effective search space: 139875 Effective search space used: 139875 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 10 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