Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate WP_013451594.1 CALNI_RS07435 glutamate-1-semialdehyde-2,1-aminomutase
Query= SwissProt::Q8ZPV2 (408 letters) >NCBI__GCF_000183405.1:WP_013451594.1 Length = 422 Score = 135 bits (341), Expect = 2e-36 Identities = 117/342 (34%), Positives = 163/342 (47%), Gaps = 31/342 (9%) Query: 22 PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIGNGYTNE 81 P RG+GS+++D GKEYID+ GHA + + + G E Sbjct: 30 PIFIDRGKGSKIYDVDGKEYIDYVCSWGPLIHGHADDDIITEVERVLKKGTTFGAPTVLE 89 Query: 82 PALRLAKKLIDATFA-ERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAFHG 140 L LAKK+++ + E V +SG EA +A++LAR Y G K I+ F+ +HG Sbjct: 90 --LELAKKVVEMVPSIEMVRMVSSGTEAVMSAIRLARGYT----GRDK--IIKFEGCYHG 141 Query: 141 RT--LFTVSAGGQPTYSQDFAP-LPPDI-RH---AAYNDLNSASALIDDNT---CAVIVE 190 + L + G T+ Q +P +P D+ +H A YNDLNS L +N VIVE Sbjct: 142 HSDSLLVKAGSGALTFGQPSSPGVPADLAKHTLIADYNDLNSVKQLFINNKNQIACVIVE 201 Query: 191 PVQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGVTPDILTT 250 PV G GV+ + FL GLR+LC ALLIFDEV TG R A ++ V PDI T Sbjct: 202 PVAGNMGVVLPEEGFLSGLRDLCSNEGALLIFDEVITGF-RLAPGGAQEYFNVMPDITTL 260 Query: 251 AKALGGGFPIGA---MLTTQDYASVMTPGTHGTTYGGNPLATAVAGKVLDIINTP---EM 304 K LGGG P+GA + S + P T GNPLA A L+ +N E+ Sbjct: 261 GKILGGGLPVGAYGGRKEIMEKISPLGPVYQAGTLSGNPLAMAAGIANLNKLNENFYYEL 320 Query: 305 QNGVRQRHDAFIERLNTLNVRFGMFSEIRGLGLLLGCVLQTE 346 + + + F L + + F+EI + C+ TE Sbjct: 321 RKKSQYLWNGFKNNCRELKLNYA-FNEIES----MSCMFFTE 357 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: 428 Number of extensions: 28 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: 422 Length adjustment: 31 Effective length of query: 377 Effective length of database: 391 Effective search space: 147407 Effective search space used: 147407 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 10 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