Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate Dsui_3250 Dsui_3250 acetylornithine/succinylornithine aminotransferase
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >FitnessBrowser__PS:Dsui_3250 Length = 390 Score = 278 bits (710), Expect = 3e-79 Identities = 165/392 (42%), Positives = 219/392 (55%), Gaps = 11/392 (2%) Query: 14 MMPVYA--PAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKF 71 +M YA P AF GEG+R++D GK Y+D GIAVN LGH HP+LV A+ QA + Sbjct: 4 LMNTYARLPVAFS--HGEGNRIYDTDGKCYLDALSGIAVNTLGHNHPKLVNAIASQAARV 61 Query: 72 WHTGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGI 131 HT N Y LA +L + + VFFCNSG EANEAA+KLAR + H + G + I Sbjct: 62 LHTSNLYRIPLQEELADRLAGLSRMEEVFFCNSGCEANEAAIKLARFFGHQK-GVDAPVI 120 Query: 132 VAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKAL--IDDNTCAVIV 189 + + AFHGRTL T+SA G F PL YNDLD+ +A ++ N AV++ Sbjct: 121 IVMEKAFHGRTLATLSATGNRKAQAGFEPLVSGFVRVPYNDLDAIRAAAELNPNVVAVLL 180 Query: 190 EPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLS 249 E +QGEGG+ AD +F RGLR LCD + LL+ DEVQ G+GRTG + + H G+ PD+ + Sbjct: 181 EMVQGEGGIHVADPEFQRGLRSLCDEKDWLLMCDEVQCGMGRTGTWFGFQHAGILPDVAT 240 Query: 250 TAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREVLNGVK 309 AK LG G PIGA + + + A + G HG+T+GGNPLACA A A I ++ Sbjct: 241 LAKGLGSGVPIGACMTAGKAAGLFKPGNHGSTFGGNPLACAAALTTIACIEEEKLRENAV 300 Query: 310 QRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEEGLMILIAG 369 + + L+ A G EIRG GL++G L D G+ A + E GL+I + Sbjct: 301 AQGEAIRRGLSEALAGVGGLVEIRGKGLMLGIEL-DRPCGELVA---KGLEAGLLINVTA 356 Query: 370 ANVVRFAPALIISEDEVNSGLDRFELACKRFL 401 VVR PAL S + + R K FL Sbjct: 357 EKVVRLLPALTFSAADTQELVQRLAALIKEFL 388 Lambda K H 0.321 0.137 0.412 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: 420 Number of extensions: 20 Number of successful extensions: 4 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: 390 Length adjustment: 31 Effective length of query: 375 Effective length of database: 359 Effective search space: 134625 Effective search space used: 134625 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