Align Succinylornithine transaminase; SOAT; EC 2.6.1.81; Succinylornithine aminotransferase (uncharacterized)
to candidate 200454 SO1276 4-aminobutyrate aminotransferase (NCBI ptt file)
Query= curated2:Q3Z295 (406 letters) >FitnessBrowser__MR1:200454 Length = 425 Score = 215 bits (547), Expect = 2e-60 Identities = 141/394 (35%), Positives = 207/394 (52%), Gaps = 31/394 (7%) Query: 22 PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGN---GY 78 P R E + +WD +G+E+IDFAGGIAV GH HP+++ A+ Q F HT GY Sbjct: 25 PIFTARAENASVWDVEGREFIDFAGGIAVLNTGHLHPKVKAAVAAQLEDFSHTCFMVLGY 84 Query: 79 TNE-PVLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNA 137 + V +L+ FA + SG+EA E A+K+AR + + ++G++AF + Sbjct: 85 ESYIQVCEKLNQLVPGDFAKKTALFTSGSEAVENAVKVARAY------TKRAGVIAFTSG 138 Query: 138 FHGRTLFTVSAGGQPA-YSQDFAPLPPDIRHA----AYNDINSASALI-------DDAT- 184 +HGRT+ ++ G+ A YS+ + ++ A A + ++ A+ +DA Sbjct: 139 YHGRTMAALALTGKVAPYSKGMGLMSANVFRAEFPCALHGVSDDDAMASIERIFKNDAEP 198 Query: 185 ---CAVIVEPIQGEGGVVPASNAFLQGLRELCDRHNALLIFDEVQTGVGRTGELYAYMHY 241 A+I+EP+QGEGG S AF+Q LR LCDR +LI DEVQTG GRTG +A Sbjct: 199 SDIAAIILEPVQGEGGFYAVSPAFMQRLRALCDREGIMLIADEVQTGAGRTGTFFAMEQM 258 Query: 242 GVTPDLLTTAKALGGGFPVGALLTTEECASVMTVGTHGTTYGGNPLASAVAGKVLELINT 301 GV+ D+ T AK++ GGFP+ + + + G G TYGGNPLA A A VLE+ Sbjct: 259 GVSADITTFAKSIAGGFPLSGITGRAQVMDAIGPGGLGGTYGGNPLACAAALAVLEVFEE 318 Query: 302 PEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNAD---YAGQAKQISQEA 358 ++L D LNT+ + ++VRGLG + L D QI EA Sbjct: 319 EKLLERANAIGDRIKSALNTMQVEHPQIADVRGLGAMNAIELMEDGKPAPQYCAQILAEA 378 Query: 359 AKAGVMVLIAG--GNVVRFAPALNVSEEEVTTGL 390 G+++L G GNV+R L VS+ ++ GL Sbjct: 379 RNRGLILLSCGTYGNVLRILVPLTVSDTQLDAGL 412 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: 463 Number of extensions: 13 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: 425 Length adjustment: 31 Effective length of query: 375 Effective length of database: 394 Effective search space: 147750 Effective search space used: 147750 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