Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 3607384 Dshi_0798 acetylornithine and succinylornithine aminotransferase (RefSeq)
Query= BRENDA::O30508 (406 letters) >FitnessBrowser__Dino:3607384 Length = 393 Score = 327 bits (837), Expect = 5e-94 Identities = 168/386 (43%), Positives = 239/386 (61%), Gaps = 5/386 (1%) Query: 17 MVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWH 76 ++P Y A V+GEG+ + + GR +D GIAV +LGHAHP LV ALT+QAQ +WH Sbjct: 5 ILPTYNRAPLSFVKGEGAWLIEADGRRFLDLGAGIAVNALGHAHPRLVAALTDQAQALWH 64 Query: 77 VSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIA 136 VSN++ +LA LV TFA+ VF NSG E+ E A K+ R++ +D P++ EI+ Sbjct: 65 VSNLYQIPAQQKLAEMLVAETFADTVFFTNSGTESCELAVKMVRKHFHDAGQPERVEILT 124 Query: 137 ASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDKTCAVVLEPIQ 196 SFHGR+ + G K + GFGP G H+P+ + EAL++A++D+T A+++EP+Q Sbjct: 125 FEGSFHGRSSAGIAAAGSEKMTKGFGPLLPGFRHLPFGNHEALQSAVNDRTAAIMVEPVQ 184 Query: 197 GEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAKS 256 GEGG+ A L+G R LCD+H L++ DEVQ G+GR G LFA+ GV PDI+ AK Sbjct: 185 GEGGIRALPDACLKGLRDLCDQHGILMILDEVQCGVGRTGRLFAHEWAGVSPDIMMVAKG 244 Query: 257 LGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKAKHE 316 +GGGFP+GA+L T + A ++ GTHG+TYGGNPL AV A L+ + L+ V+ K Sbjct: 245 IGGGFPLGAVLATADAASGMTAGTHGSTYGGNPLGCAVGCAVLETVCADGFLEEVRRKAG 304 Query: 317 RFKSRLQKIGQEY-GIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQASPDV 375 + L+ + E+ G+F E+RG GL++G + DV+ A V+V+ A+ +V Sbjct: 305 LMRQALEGLVAEFPGVFAEVRGAGLMLGLVC----RAPNTDVVQAGYGAEVLVVPAAENV 360 Query: 376 VRFAPSLVIDDAEIDEGLERFERAVA 401 VR P L I DAEI E L R +A A Sbjct: 361 VRLLPPLTITDAEIREALARLRKAAA 386 Lambda K H 0.318 0.135 0.394 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: 405 Number of extensions: 22 Number of successful extensions: 3 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: 393 Length adjustment: 31 Effective length of query: 375 Effective length of database: 362 Effective search space: 135750 Effective search space used: 135750 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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