Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate Synpcc7942_0645 Synpcc7942_0645 glutamate-1-semialdehyde aminotransferase
Query= SwissProt::Q8ZPV2 (408 letters) >FitnessBrowser__SynE:Synpcc7942_0645 Length = 453 Score = 140 bits (354), Expect = 6e-38 Identities = 110/313 (35%), Positives = 147/313 (46%), Gaps = 27/313 (8%) Query: 22 PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIGNGYTNE 81 P + R + + WD G YID+ G GHAHP + EAL + G E Sbjct: 61 PIVFDRVKDAYAWDVDGNRYIDYVGTWGPAICGHAHPEVIEALKVAMEKGTSFGAPCALE 120 Query: 82 PALRLAKKLIDATFA-ERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAFHG 140 L A+ +IDA + E V F NSG EA A L+L R Y G K I+ F+ +HG Sbjct: 121 NVL--AEMVIDAVPSIEMVRFVNSGTEACMAVLRLMRAYT----GRDK--IIKFEGCYHG 172 Query: 141 RT-LFTVSAG-GQPTYSQDFAPLPP-----DIRHAAYNDLNSASALIDDNT---CAVIVE 190 +F V AG G T +P P + A YNDL + AL +N VI+E Sbjct: 173 HADMFLVKAGSGVATLGLPDSPGVPKSTTANTLTAPYNDLEAVKALFAENPGEIAGVILE 232 Query: 191 PVQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGVTPDILTT 250 P+ G G I FL+GLRE+ H ALL+FDEV TG R +GVTPD+ T Sbjct: 233 PIVGNSGFIVPDAGFLEGLREITLEHDALLVFDEVMTGF-RIAYGGVQEKFGVTPDLTTL 291 Query: 251 AKALGGGFPIGAMLTTQDYASVMTPG---THGTTYGGNPLATAVAGKVLDIINTPEMQNG 307 K +GGG P+GA ++ ++ P T GNPLA K L+++ P G Sbjct: 292 GKIIGGGLPVGAYGGKREIMQLVAPAGPMYQAGTLSGNPLAMTAGIKTLELLRQP----G 347 Query: 308 VRQRHDAFIERLN 320 + D +RL+ Sbjct: 348 TYEYLDQITKRLS 360 Lambda K H 0.320 0.137 0.413 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: 438 Number of extensions: 21 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: 408 Length of database: 453 Length adjustment: 32 Effective length of query: 376 Effective length of database: 421 Effective search space: 158296 Effective search space used: 158296 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: 51 (24.3 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