Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate WP_057509163.1 ABB28_RS13760 glutamate-1-semialdehyde-2,1-aminomutase
Query= SwissProt::Q8ZPV2 (408 letters) >NCBI__GCF_001431535.1:WP_057509163.1 Length = 426 Score = 142 bits (358), Expect = 2e-38 Identities = 102/295 (34%), Positives = 143/295 (48%), Gaps = 23/295 (7%) Query: 22 PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIGNGYTNE 81 PF R +G+ L D G YID+ G +GH HPA+R+A+ + A+ G E Sbjct: 35 PFFVERADGAYLHDVDGNRYIDYVGSWGPMIVGHNHPAVRQAVKKAADSGLSFGAPCAAE 94 Query: 82 PAL-RLAKKLIDATFAERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAFHG 140 + +L+ + E V NSG EA +A++LAR +S IV F+ +HG Sbjct: 95 VTMAETLTRLVPS--CEMVRMVNSGTEATLSAIRLARG------ATGRSRIVKFEGCYHG 146 Query: 141 R-TLFTVSAG------GQPTYSQDFAPLPPDIRHAAYNDLNSASALID---DNTCAVIVE 190 F V AG G PT A L YND ++A+AL + + +I+E Sbjct: 147 HGDSFLVKAGSGMLTLGVPTSPGVPAGLSELTLTLPYNDFDAATALFEAQGEQIAGLIIE 206 Query: 191 PVQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGVTPDILTT 250 PV G IP + +LQ LR LC R +LIFDEV TG R A HYGVTPD+ T Sbjct: 207 PVVGNANCIPPREGYLQHLRALCTRFGTVLIFDEVMTGF-RVALGGAQAHYGVTPDLTTF 265 Query: 251 AKALGGGFPIGAMLTTQDYASVMTPG---THGTTYGGNPLATAVAGKVLDIINTP 302 K +GGG P+GA ++ ++P T GNP+A A +L+++ P Sbjct: 266 GKIIGGGMPVGAYGGKRELMQQISPAGPIYQAGTLSGNPVAMAAGLAMLELVQQP 320 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: 474 Number of extensions: 26 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: 426 Length adjustment: 31 Effective length of query: 377 Effective length of database: 395 Effective search space: 148915 Effective search space used: 148915 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