Align Succinylornithine transaminase; SOAT; EC 2.6.1.81; Succinylornithine aminotransferase (uncharacterized)
to candidate BWI76_RS26375 BWI76_RS26375 aspartate aminotransferase family protein
Query= curated2:Q3Z295 (406 letters) >FitnessBrowser__Koxy:BWI76_RS26375 Length = 421 Score = 229 bits (584), Expect = 1e-64 Identities = 145/395 (36%), Positives = 204/395 (51%), Gaps = 33/395 (8%) Query: 27 RGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTN-EPVLR 85 + E + LWD +G E IDFA GIAV GH HP++ A+ +Q F HT E + Sbjct: 28 KAENATLWDIEGNEVIDFAAGIAVLNTGHRHPKIIAAVEQQLQAFTHTAYQIVPYESYVT 87 Query: 86 LAKKLIDATFAD---RVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNAFHGRT 142 LA+++ D + F +GAEA E A+K+AR + + + G++ F FHGRT Sbjct: 88 LAERINALAPIDGPAKTAFFTTGAEAVENAVKIARAY------TGRPGLITFGGGFHGRT 141 Query: 143 LFTVSAGGQPA-YSQDFAPLPPDIRHAAY----NDINSASALID-----------DATCA 186 T++ G+ A Y F P P + HA Y + I +A A+ D A Sbjct: 142 FMTMALTGKVAPYKIGFGPFPGSVYHAVYPNAAHGITTADAMKSLDRIFKADIAADQVAA 201 Query: 187 VIVEPIQGEGGVVPASNAFLQGLRELCDRHNALLIFDEVQTGVGRTGELYAYMHYGVTPD 246 +++EPIQGEGG A F+Q LR LCD H LLI DEVQTG RTG+L+A HY V PD Sbjct: 202 IVLEPIQGEGGFNVAPPEFMQALRALCDTHGILLIADEVQTGFARTGKLFAMQHYDVKPD 261 Query: 247 LLTTAKALGGGFPVGALLTTEECASVMTVGTHGTTYGGNPLASAVAGKVLELINTPEMLN 306 L+T AK+L GGFP+ ++ E G G TY GNPLA A A VL++I ++ Sbjct: 262 LMTMAKSLAGGFPLSGVVGRAEVMDAPAPGGLGGTYAGNPLAVAAAHAVLDVIEEEQLCQ 321 Query: 307 GVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQ-----AKQISQEAAKA 361 ++ E LN ++VRG G ++ N G+ +QI Q+A + Sbjct: 322 RAERLGSHLKEVLNQARQSCPAIADVRGQGSMVAVEFNDPQTGEPSAEITRQIQQKAQEN 381 Query: 362 GVMVLIAG--GNVVRFAPALNVSEEEVTTGLDRFA 394 G+++L G GNV+RF L + + + T LD A Sbjct: 382 GLLLLSCGVYGNVIRFLYPLTIPDAQFTKALDILA 416 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: 448 Number of extensions: 21 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: 421 Length adjustment: 31 Effective length of query: 375 Effective length of database: 390 Effective search space: 146250 Effective search space used: 146250 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.
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