Align Succinylornithine transaminase; SOAT; EC 2.6.1.81; Succinylornithine aminotransferase (uncharacterized)
to candidate BPHYT_RS10155 BPHYT_RS10155 2,2-dialkylglycine decarboxylase
Query= curated2:Q3Z295 (406 letters) >FitnessBrowser__BFirm:BPHYT_RS10155 Length = 433 Score = 189 bits (480), Expect = 1e-52 Identities = 137/412 (33%), Positives = 203/412 (49%), Gaps = 42/412 (10%) Query: 22 PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNE 81 P I R +GS ++D G+ +DF G LGH+HPE+ +NE A K H +G + Sbjct: 26 PMIIERAQGSFVYDADGRAILDFTSGQMSAVLGHSHPEIVSVINEYAGKLDHLFSGMLSR 85 Query: 82 PVLRLAKKLIDAT--FADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNAFH 139 PV+ LA +L + T DR ++GAE+NEAA+++A+ + K IV F ++H Sbjct: 86 PVVDLATRLAEITPDGLDRALLLSTGAESNEAAIRMAKLV------TGKYEIVGFAQSWH 139 Query: 140 GRTLFTVSA-------GGQPAYSQDFAPLPPDI------RHAAYN---DINSASALIDDA 183 G T SA G PA FA P + RH Y+ +++ A LID Sbjct: 140 GMTAAAASATYSAGRKGVGPAAVGSFAIPAPFLYRPRFERHGDYDYLAELDYAFDLIDRQ 199 Query: 184 T----CAVIVEPIQGEGGVVPASNAFLQGLRELCDRHNALLIFDEVQTGVGRTGELYAYM 239 + A I EPI GG++ ++ L+ C+ LLI DE QTGVGRTG ++A Sbjct: 200 SSGNLAAFIAEPILSSGGIIELPEGYMTALKRKCEERGMLLILDEAQTGVGRTGTMFACQ 259 Query: 240 HYGVTPDLLTTAKALGGGFPVGALLTT---EECASVMTVGTHGTTYGGNPLASAVAGKVL 296 GVTPD+LT +K LG G P+ A++T+ EE A + + TT+ +PL +AV +VL Sbjct: 260 RDGVTPDILTLSKTLGAGLPLAAVVTSAQIEERAHELGYLFY-TTHVSDPLPAAVGLRVL 318 Query: 297 ELINTPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYA------GQ 350 E++ ++ L + R+ ++RG GLL+G + D G Sbjct: 319 EVVERDGLVARANLMGARLKRGLLDLMERFDCIGDIRGRGLLLGMEIVKDRRTKEPADGL 378 Query: 351 AKQISQEAAKAG----VMVLIAGGNVVRFAPALNVSEEEVTTGLDRFAAACE 398 +I++E G ++ L G V R AP L V E+E+ GLD A E Sbjct: 379 GAKITRECMNLGLSMNIVQLPGMGGVFRIAPPLTVHEDEIDLGLDLLGQAIE 430 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: 395 Number of extensions: 19 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: 433 Length adjustment: 32 Effective length of query: 374 Effective length of database: 401 Effective search space: 149974 Effective search space used: 149974 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