Align Succinylornithine transaminase; SOAT; EC 2.6.1.81; Succinylornithine aminotransferase (uncharacterized)
to candidate AZOBR_RS19630 AZOBR_RS19630 4-aminobutyrate aminotransferase
Query= curated2:Q3Z295 (406 letters) >FitnessBrowser__azobra:AZOBR_RS19630 Length = 428 Score = 226 bits (577), Expect = 8e-64 Identities = 154/418 (36%), Positives = 218/418 (52%), Gaps = 42/418 (10%) Query: 15 IPVYAPAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHT 74 +PVY R E + LWD +G +IDFAGGIAV GH HP++ EA+ Q +F HT Sbjct: 22 MPVYVD------RAENAELWDVEGNRFIDFAGGIAVLNTGHRHPKIIEAVKAQLDRFTHT 75 Query: 75 GNGYTN-EPVLRLAKKL---IDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSG 130 T E + LA++L + + + F +GAEA E A+K+AR AH + + G Sbjct: 76 CAMVTPYESFVTLAERLNALVPGSTPKKTAFFTTGAEAVENAVKIAR--AH----TGRPG 129 Query: 131 IVAFKNAFHGRTLFTVSAGGQPA-YSQDFAPLPPDIRHAAYNDINSASALID-------- 181 ++AF AFHGRTL ++ G+ Y F P P ++ HA + + ++ D Sbjct: 130 VIAFSGAFHGRTLLAMALTGKVVPYKVGFGPFPAEVYHAPFPNAYRGVSVQDSLKALEQL 189 Query: 182 -----DAT--CAVIVEPIQGEGGVVPASNAFLQGLRELCDRHNALLIFDEVQTGVGRTGE 234 DAT A+IVEP+QGEGG A FLQ LR++CD + LLI DE+QTG RTG+ Sbjct: 190 FKSDVDATRVAAIIVEPVQGEGGFNIAPPEFLQALRKICDENGILLIIDEIQTGFARTGK 249 Query: 235 LYAYMHYGVTPDLLTTAKALGGGFPVGALLTTEECASVMTVGTHGTTYGGNPLASAVAGK 294 ++A H GV PDL+T AK+L GGFP+ A+ E G G TY G+PLA+ A Sbjct: 250 MFAIEHSGVEPDLMTMAKSLAGGFPLSAVTGKAEIMDAPIPGGIGGTYAGSPLATTAALA 309 Query: 295 VLELINTPEMLNGVKQRHDWFVERLNTINHR--YGLFSEVRGLGLLIGCVLNAD------ 346 VL++I +++ + R T+ R + +VR LG +I L D Sbjct: 310 VLDVIEEEKLIQRSNDLGERIAGRFRTMAQRNTLSVIGDVRNLGGMIAMELVKDRGTKEP 369 Query: 347 YAGQAKQISQEAAKAGVMVLIAG--GNVVRFAPALNVSEEEVTTGLDRFAAACEHFVS 402 A K + +AA+ G+++L G GNV+R L S+ V GLD + E VS Sbjct: 370 AAELTKALVAKAAEKGLVLLSCGTYGNVIRILVPLTASDALVDEGLDIIERSLEELVS 427 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: 457 Number of extensions: 18 Number of successful extensions: 5 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: 428 Length adjustment: 31 Effective length of query: 375 Effective length of database: 397 Effective search space: 148875 Effective search space used: 148875 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