Align Succinylornithine transaminase; SOAT; EC 2.6.1.81; Succinylornithine aminotransferase (uncharacterized)
to candidate RR42_RS21370 RR42_RS21370 4-aminobutyrate aminotransferase
Query= curated2:Q3Z295 (406 letters) >FitnessBrowser__Cup4G11:RR42_RS21370 Length = 420 Score = 228 bits (581), Expect = 3e-64 Identities = 149/400 (37%), Positives = 208/400 (52%), Gaps = 36/400 (9%) Query: 23 FIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNEP 82 F R E S +WD +GK YIDFA GIAV GH HP L EA+ Q +F HT Y P Sbjct: 24 FFAERAENSEIWDVEGKRYIDFAAGIAVLNTGHRHPRLVEAMQRQLERFTHTA--YQIVP 81 Query: 83 V---LRLAKKL---IDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKN 136 + LA+++ A + F +GAEA E A+K+AR + + G++AF Sbjct: 82 YASYIELAERINQRAPGRGAKKTAFFTTGAEAVENAIKIARA------ATGRPGVIAFSG 135 Query: 137 AFHGRTLFTVSAGGQPA-YSQDFAPLPPDIRHAAY----NDINSASAL----------ID 181 FHGRT+ ++ G+ Y F P P ++ HA Y + ++ AL +D Sbjct: 136 GFHGRTMMGMALTGKVVPYKVGFGPFPGEVFHAPYPCALHGVSVEDALKAMEHLFKADVD 195 Query: 182 DA-TCAVIVEPIQGEGGVVPASNAFLQGLRELCDRHNALLIFDEVQTGVGRTGELYAYMH 240 A+I EP+QGEGG A AF++ LR +CD H LL+ DEVQTG GRTG+L+A H Sbjct: 196 PKRVAAIIFEPVQGEGGFNVAPPAFVKALRAICDEHGILLVADEVQTGFGRTGKLFAMEH 255 Query: 241 YGVTPDLLTTAKALGGGFPVGALLTTEECASVMTVGTHGTTYGGNPLASAVAGKVLELIN 300 Y V PDL T AK+L GG P+ A+ E G G TY GNPLA A A VL+++ Sbjct: 256 YDVAPDLTTMAKSLAGGMPLSAVCGRAEVMDAPAPGGLGGTYAGNPLAVASALAVLDVLE 315 Query: 301 TPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVL-NADYAGQA---KQISQ 356 +++ V RL + R +E+RGLG ++ AD A A +++ Sbjct: 316 GEQLIPRGAALGQRLVARLEALKARVPQIAEIRGLGAMVAVEFRRADGAPDAEFTREVQN 375 Query: 357 EAAKAGVMVLIAG--GNVVRFAPALNVSEEEVTTGLDRFA 394 A + G+++L G GNV+RF L +S+ + GLD A Sbjct: 376 RALEQGLLLLSCGVYGNVIRFLFPLTISDAVMNEGLDILA 415 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: 455 Number of extensions: 28 Number of successful extensions: 7 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: 420 Length adjustment: 31 Effective length of query: 375 Effective length of database: 389 Effective search space: 145875 Effective search space used: 145875 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