Align succinylornithine transaminase; EC 2.6.1.81 (characterized)
to candidate Dsui_0023 Dsui_0023 acetylornithine/succinylornithine aminotransferase
Query= CharProtDB::CH_002469 (406 letters) >FitnessBrowser__PS:Dsui_0023 Length = 396 Score = 293 bits (750), Expect = 6e-84 Identities = 165/362 (45%), Positives = 220/362 (60%), Gaps = 9/362 (2%) Query: 28 GEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNEPVLRLA 87 G GS L DQQGK Y+DF G AVN LGH HP + EAL QA K + + NEP L+LA Sbjct: 28 GRGSWLVDQQGKRYLDFVQGWAVNCLGHGHPAIVEALASQAGKLINPSPAFYNEPSLKLA 87 Query: 88 KKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSG---IVAFKNAFHGRTLF 144 L + DRVFF ++GAEANE A+KLARK+ HK G I+ F FHGRTL Sbjct: 88 AGLAAHSCFDRVFFASTGAEANEGAIKLARKWGQ----KHKGGAHEIITFAGGFHGRTLA 143 Query: 145 TVSAGGQPAYSQDFAPLPADIRHAAYNDINSASALIDDSTCAVIVEPIQGEGGVVPASNA 204 T+SA G+P + FAP A ND++S +ALI++ T A+++EPIQGEGGVVPAS Sbjct: 144 TMSASGKPGWDTLFAPQVPGFPKAQLNDLDSVAALINERTVAIMLEPIQGEGGVVPASAE 203 Query: 205 FLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLTTAKALGGGFPVGALL 264 FLQ LR++C+ LLI DEVQTG+GRTG+L+A+ H G+ PD++T K +GGG P+ ALL Sbjct: 204 FLQLLRQICDDRGLLLIVDEVQTGMGRTGKLFAHQHAGIEPDIMTLGKGIGGGVPLSALL 263 Query: 265 ATEECARVMTVGTHGTTYGGNPLASAVAGKVLELINTPEMLNGVKQRHDWFVERLNTINH 324 A E G G TY GNPL +AV VLE++ P L V + ++ L ++ Sbjct: 264 AKESVC-CFEAGDQGGTYNGNPLMTAVGAAVLEVLTAPGFLAEVAAKGEYLGAGLQRLSD 322 Query: 325 RYGLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAKAGVMVLIAGGNVVRFAPALNVSEE 384 R GL E RG GLL +L + + ++E G+++ +++RF P+L VS E Sbjct: 323 RLGLRGE-RGQGLLRALLLADERGPAIVEAARERGPEGLLLNAPRPHLLRFMPSLTVSRE 381 Query: 385 EV 386 E+ Sbjct: 382 EI 383 Lambda K H 0.319 0.136 0.407 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: 469 Number of extensions: 23 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: 396 Length adjustment: 31 Effective length of query: 375 Effective length of database: 365 Effective search space: 136875 Effective search space used: 136875 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 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