Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_101444294.1 BD749_RS10520 ornithine--oxo-acid transaminase
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_002846395.1:WP_101444294.1 Length = 413 Score = 245 bits (626), Expect = 2e-69 Identities = 143/395 (36%), Positives = 213/395 (53%), Gaps = 9/395 (2%) Query: 14 DRYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQR 73 ++Y NY P + +GEG +WD G+ DF + + GH HP ++ AL EQAQ+ Sbjct: 17 EKYGAHNYHPLPVVLSKGEGVYLWDVEGKRYYDFLSAYSAVNQGHCHPRIINALIEQAQQ 76 Query: 74 IWHVSNVFTNEPALRLARKLVDATFA-ERVFLANSGAEANEAAFKLARR--YANDVYGPQ 130 + S F N+ L +A K + F ++ NSGAEA E A KLAR+ Y P Sbjct: 77 LTLTSRAFYNDK-LGIAEKYICELFGYDKSLYMNSGAEAVETAIKLARKWGYLKKGIAPH 135 Query: 131 KYEIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDK--TC 188 EII +FHGRT ++ P + GFGP G +PYNDLEAL+ A+ + C Sbjct: 136 NAEIIVVERNFHGRTTGIISFSTDPDSTKGFGPYMPGFKVIPYNDLEALETALKENPNVC 195 Query: 189 AVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVP 248 ++EPIQGE GV+ Q YL A LC E+N LL+ DE+Q+G+ R G++ A + V Sbjct: 196 GFLVEPIQGEAGVVVPQDGYLAKAHALCKEYNVLLMADEIQTGIARTGKMLASYYDDVKA 255 Query: 249 DILSSAKSLGGG-FPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEV 307 DIL K+L GG P+ +L +I + G HG+T+GGNP+A+AVA AAL+VI + Sbjct: 256 DILILGKALSGGVLPVSCVLANDDIMLCIQPGEHGSTFGGNPMAAAVAIAALEVIKEENL 315 Query: 308 LDGVKAKHERFKSRLQKI-GQEYGIFDEIRGMGLLIGAALTDEWKGK-ARDVLNAAEKEA 365 ++ E F+ R+ ++ + + +RG GLL + G+ A DV ++ Sbjct: 316 VENAYKLGEIFRDRMNQLKAKRPEVVTLVRGRGLLNAIVIEPAADGRTAWDVCVELKENG 375 Query: 366 VMVLQASPDVVRFAPSLVIDDAEIDEGLERFERAV 400 ++ D++RFAP LV+ + ++ E + ER V Sbjct: 376 LLAKPTHGDIIRFAPPLVMTEEQLHECCDIIERVV 410 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: 418 Number of extensions: 22 Number of successful extensions: 6 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: 413 Length adjustment: 31 Effective length of query: 375 Effective length of database: 382 Effective search space: 143250 Effective search space used: 143250 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 Jul 26 2024. The underlying query database was built on Jul 25 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