Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_013835847.1 THICY_RS06630 aspartate aminotransferase family protein
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_000214825.1:WP_013835847.1 Length = 390 Score = 272 bits (695), Expect = 1e-77 Identities = 156/378 (41%), Positives = 226/378 (59%), Gaps = 18/378 (4%) Query: 31 GEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWHVSNVFTNEPALRLA 90 GEG+ ++D+ +D GIAV SLGHAHPA+ +AL EQ++ + H SN++ +L Sbjct: 18 GEGALLYDEQDNAYLDAVSGIAVCSLGHAHPAIAQALCEQSKTLIHTSNLYHVAKQQQLG 77 Query: 91 RKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAASNSFHGRTLFTVN 150 KLV + ++VF NSGAEANEAA K+AR+Y + G +II NSFHGRTL T++ Sbjct: 78 DKLVAISGMDKVFFGNSGAEANEAAIKMARKYGHSK-GISHAQIIVMENSFHGRTLATLS 136 Query: 151 VGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDK--TCAVVLEPIQGEGGVLPAQQAY 208 G K DGF P EG VP++++EA+ AI++ A+++EP+QGEGGV + Y Sbjct: 137 ATGSAKVHDGFYPLVEGFVRVPFDNVEAVANAIANNPNVVAILVEPVQGEGGVHVPKPGY 196 Query: 209 LEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAKSLGGGFPIGAMLT 268 L+ R LCDEH+ LL+ DE+Q+G+GR G+ FA+ H G++PD+LS AK+LG G PIGA L Sbjct: 197 LKALRALCDEHDLLLMIDEIQAGIGRTGKWFAFQHEGILPDVLSLAKALGNGVPIGASLA 256 Query: 269 TGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKAKHER----FKSRLQK 324 G+ A+ + G HGTT+GGNPLA A A ++ + +D V + FK+ L Sbjct: 257 RGKAAELFAPGNHGTTFGGNPLACAAGLAVIETLEYHNYIDLVAKQGAELLAAFKTALAN 316 Query: 325 IGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQASPDVVRFAPSLVI 384 I G+ D IRG G +IG L D++ A + +++ D VR P+ V+ Sbjct: 317 IP---GVVD-IRGKGYMIGIQL----DRPCGDLVKMALADKLLINVTRGDTVRLLPTFVM 368 Query: 385 DDAEIDE---GLERFERA 399 A+ ++ GL R +A Sbjct: 369 THAQSEQLVNGLTRLIKA 386 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: 413 Number of extensions: 25 Number of successful extensions: 3 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: 390 Length adjustment: 31 Effective length of query: 375 Effective length of database: 359 Effective search space: 134625 Effective search space used: 134625 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