Align Succinylornithine transaminase; SOAT; EC 2.6.1.81; Succinylornithine aminotransferase (uncharacterized)
to candidate 208688 DVU3168 glutamate-1-semialdehyde-2,1-aminomutase
Query= curated2:Q3Z295 (406 letters) >MicrobesOnline__882:208688 Length = 423 Score = 147 bits (372), Expect = 4e-40 Identities = 118/319 (36%), Positives = 153/319 (47%), Gaps = 32/319 (10%) Query: 22 PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNE 81 P R GSRL G+ +IDF LGH HPE+ A++ + T G E Sbjct: 34 PLFIARAAGSRLHTVDGETFIDFVESWGPMLLGHTHPEVTAAVHAAVDR--GTSYGAPCE 91 Query: 82 PVLRLAKKLIDAT-FADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNAFHG 140 + LA K++DA D V NSG EA +AL+LAR + + ++ +V F +HG Sbjct: 92 DEVVLAAKVVDALPGVDMVRMVNSGTEATMSALRLARGY------TGRTKLVKFVGCYHG 145 Query: 141 RT-LFTVSAG-GQPAYSQDFAPLPP-----DIRHAAYNDINSAS---ALIDDATCAVIVE 190 F SAG G S P P D A YND+ + AL A+IVE Sbjct: 146 HADPFLASAGSGVATLSIPGTPGVPESTVRDTLLAPYNDLAAVKDLFALHGKDIAAIIVE 205 Query: 191 PIQGEGGVVPASNAFLQGLRELCDRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLTT 250 + G G+VP FL+GLRELCD+H ALLIFDEV TG R A +G+TPDL T Sbjct: 206 AVAGNMGLVPPKAGFLEGLRELCDQHGALLIFDEVITGF-RVSFGGAQQRFGITPDLTTL 264 Query: 251 AKALGGGFPVGALLTTEE-------CASVMTVGTHGTTYGGNPLASAVAGKVLELINTPE 303 K +GGG PVGA E C V G T GNPLA A L++++ + Sbjct: 265 GKIIGGGLPVGAYGGKREIMQRIAPCGEVYQAG----TLSGNPLAMAAGIATLDVLSRSD 320 Query: 304 MLNGVKQRHDWFVERLNTI 322 G++ R FV+ L I Sbjct: 321 YA-GLEARVAAFVKELEAI 338 Lambda K H 0.319 0.136 0.408 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: 431 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 406 Length of database: 423 Length adjustment: 31 Effective length of query: 375 Effective length of database: 392 Effective search space: 147000 Effective search space used: 147000 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 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