Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 199805 SO0617 acetylornithine aminotransferase (NCBI ptt file)
Query= BRENDA::O30508 (406 letters) >FitnessBrowser__MR1:199805 Length = 405 Score = 532 bits (1371), Expect = e-156 Identities = 257/397 (64%), Positives = 321/397 (80%) Query: 7 QVERADFDRYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKA 66 ++ RA FD MVPNYAPAA IPVRGEGSRVWDQ G E IDFAGGIAV LGH HPALV A Sbjct: 6 KLNRAQFDAVMVPNYAPAAVIPVRGEGSRVWDQEGNEFIDFAGGIAVNCLGHCHPALVNA 65 Query: 67 LTEQAQRIWHVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDV 126 L Q +++WH+SNV TNEPAL LA KLV++TFAERV+ ANSGAEANEAA KLARRYA + Sbjct: 66 LKTQGEKLWHLSNVMTNEPALELATKLVNSTFAERVYFANSGAEANEAALKLARRYALEK 125 Query: 127 YGPQKYEIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDK 186 +G +K EIIA +FHGRT FTV+VGGQ YSDGFGPK + ITH+P+ND+ AL+AA+SDK Sbjct: 126 HGVEKDEIIAFDKAFHGRTFFTVSVGGQAAYSDGFGPKPQSITHLPFNDVAALEAAVSDK 185 Query: 187 TCAVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGV 246 TCA++LEP+QGEGG++ A A+L+ R+L ++HNAL++FDEVQ+G+GR GEL+AYM + Sbjct: 186 TCAIMLEPLQGEGGIIDADPAFLKAVRELANKHNALVIFDEVQTGVGRTGELYAYMGTDI 245 Query: 247 VPDILSSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPE 306 VPDIL++AK+LGGGFPI AMLTT EIA+HL VGTHG+TYGGNPLA A+ A LDV+NTPE Sbjct: 246 VPDILTTAKALGGGFPIAAMLTTTEIAEHLKVGTHGSTYGGNPLACAIGNAVLDVVNTPE 305 Query: 307 VLDGVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAV 366 VL+GVK + + + L KI ++Y +F E+RG GLL+GA L ++++G++RD L A+ E + Sbjct: 306 VLNGVKHREQLLRDGLNKINEKYHVFSEVRGKGLLLGAVLNEQYQGRSRDFLVASVAEGL 365 Query: 367 MVLQASPDVVRFAPSLVIDDAEIDEGLERFERAVAKL 403 M L A +VVRFAPSLVI +A+I EGL RFERAVA + Sbjct: 366 MSLMAGANVVRFAPSLVIPEADIAEGLARFERAVASI 402 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: 528 Number of extensions: 12 Number of successful extensions: 1 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: 405 Length adjustment: 31 Effective length of query: 375 Effective length of database: 374 Effective search space: 140250 Effective search space used: 140250 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 Aug 03 2021. The underlying query database was built on Aug 03 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