Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate WP_013835162.1 THICY_RS03115 diaminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::Q8ZPV2 (408 letters) >NCBI__GCF_000214825.1:WP_013835162.1 Length = 428 Score = 168 bits (426), Expect = 2e-46 Identities = 124/407 (30%), Positives = 192/407 (47%), Gaps = 48/407 (11%) Query: 35 DQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIGNGYTNE-PALRLAKKLIDA 93 D +GK YIDF GG GH HP + +AL R NG TN +AK + Sbjct: 34 DVEGKRYIDFFGGAGSLNYGHNHPLINQALITYIQR-----NGITNALDKATVAKHDFIS 88 Query: 94 TFAERV-----------FFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAFHGRT 142 F + F +GA E ALKLARK +S ++AF NA+HG + Sbjct: 89 AFQSIILKPRKMDYKIQFVGPTGANGVETALKLARKM------KKRSNVIAFTNAYHGHS 142 Query: 143 LFTVSAGGQPTYSQDFAPLPPDIRHAAYN-----DLNSASAL---IDDNT------CAVI 188 L ++ G Y D+ +P ++ Y+ D++S L + D + AVI Sbjct: 143 LGALAVTGNEFYHGDYYDVPRNVNKMPYDNYFDHDMDSVDMLRHYLGDGSSGYELPAAVI 202 Query: 189 VEPVQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGVTPDIL 248 VE +QGEGG+ A+ +LQ L LC LLI DE+Q G GRTG+ +++ G+ PDI+ Sbjct: 203 VESIQGEGGINVASVGWLQKLSALCKEMDILLIMDEIQVGNGRTGDYFSFERAGIMPDII 262 Query: 249 TTAKALGGGFPIGAMLTTQDYASVMTPGTHGTTYGGNPLATAVAGKVLDIINTPEMQNGV 308 T +K++G G P+ +L + V +PG H T+ GN A L++ + + Sbjct: 263 TLSKSIGTGMPMSIVL-MKPSVDVWSPGEHTGTFRGNSYAFIAGAAALELWRNDDFSRSI 321 Query: 309 RQRHDAFIERLNTLNVRF-GMFSEIRGLGLLLGCVLQTEFAGKAKLIAQEAAKAGVMVLI 367 R + RF G +++RGLG++ G L++ G ++++A + G+M+ Sbjct: 322 RAKGKQVEAAFKDFQARFPGWITDVRGLGMIWG--LESLVEGFCNEVSKQAFQRGLMMET 379 Query: 368 AGG--DVVRFAPALNVSDEEIATGLD-----RFALACERLQTGGVPC 407 AG V++F L +S+ E+ G + A +TG PC Sbjct: 380 AGASDQVLKFLGPLVISETELNEGFEILTDAILAAVAVFEKTGRTPC 426 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: 415 Number of extensions: 27 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: 428 Length adjustment: 32 Effective length of query: 376 Effective length of database: 396 Effective search space: 148896 Effective search space used: 148896 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