Align Succinylornithine transaminase; SOAT; EC 2.6.1.81; Succinylornithine aminotransferase (uncharacterized)
to candidate 5210744 Shew_3172 4-aminobutyrate aminotransferase (RefSeq)
Query= curated2:Q3Z295 (406 letters) >FitnessBrowser__PV4:5210744 Length = 426 Score = 228 bits (582), Expect = 2e-64 Identities = 150/409 (36%), Positives = 213/409 (52%), Gaps = 35/409 (8%) Query: 22 PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTG---NGY 78 P R + LWD +GK YIDF GIAV GH+HP++ A+ Q F HT N Y Sbjct: 23 PVYVERALNAELWDVEGKRYIDFGTGIAVCNTGHSHPKVVAAVKAQLDNFSHTCVMVNPY 82 Query: 79 TNEPVLRLAKKLIDATFADR-VFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNA 137 + L I +D+ F +GAEA E +K+AR AH + + G++AF Sbjct: 83 ESAVALAEQLNRIAPGGSDKKAIFVTTGAEAVENCVKIAR--AH----TGRRGVIAFNGG 136 Query: 138 FHGRTLFTVSAGGQ-PAYSQDFAPLPPDIRHA----AYNDINSASAL--------IDDAT 184 FHGRT T++ G+ Y F P DI HA A++ ++ +L +D A Sbjct: 137 FHGRTNLTMALTGKITPYKHQFGPFAGDIFHAPYPVAFHGVSVKDSLKAIEHLFKVDIAP 196 Query: 185 C---AVIVEPIQGEGGVVPASNAFLQGLRELCDRHNALLIFDEVQTGVGRTGELYAYMHY 241 C A++VEP+QGEGG A FLQ LR LCD+H +L+ DE+QTG GRTG++++ H Sbjct: 197 CDVAAIVVEPVQGEGGFYAAPPEFLQALRALCDQHGIVLVMDEIQTGFGRTGKMFSCEHA 256 Query: 242 GVTPDLLTTAKALGGGFPVGALLTTEECASVMTVGTHGTTYGGNPLASAVAGKVLELINT 301 GV PDL+T AK + GGFP+ A++ E G G TYGG+P+ A VLE++ Sbjct: 257 GVEPDLMTMAKGIAGGFPLAAVVGKSEIMDAPLPGGLGGTYGGSPVGCVAALAVLEVMQE 316 Query: 302 PEMLNGVKQRHDWFVERLNTINHRY-GLFSEVRGLGLLIGCVLNAD------YAGQAKQI 354 +++ + D F + L+ + +Y L EVR G +I L D + I Sbjct: 317 EQLVERAVKIGDSFNQALSALKEQYPQLIGEVRNQGAMIAMELVIDGDIEQPNTALTQAI 376 Query: 355 SQEAAKAGVMVLIAG--GNVVRFAPALNVSEEEVTTGLDRFAAACEHFV 401 AA G+++L G GNV+RF PAL +S+E + GL +F E V Sbjct: 377 IANAAAHGLVLLACGFYGNVIRFLPALTISDEIMAEGLAKFKTLFESLV 425 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: 468 Number of extensions: 18 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: 426 Length adjustment: 31 Effective length of query: 375 Effective length of database: 395 Effective search space: 148125 Effective search space used: 148125 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