Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_013074657.1 BTUS_RS03025 aspartate aminotransferase family protein
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_000092905.1:WP_013074657.1 Length = 466 Score = 231 bits (590), Expect = 3e-65 Identities = 150/399 (37%), Positives = 209/399 (52%), Gaps = 22/399 (5%) Query: 13 FDRYMVPNYAPAAFI------PVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKA 66 +D Y+ P A + +RGEGS V+D+ G+ ID G GH +++A Sbjct: 11 YDSYINPGLAKLYHLMGLSAGELRGEGSVVYDEDGKRYIDCVSGYGSLPFGHCPRPVLEA 70 Query: 67 LTEQAQRIWHVSNVFTNEPALRLARKLVDATFAERV--FLANSGAEANEAAFKLARRYAN 124 + Q R+ S V PA LA L T + F NSGAEA E A KLAR Sbjct: 71 VRRQMDRMALSSKVMPGRPAGELAEALAGWTPGDLQYSFFCNSGAEAVEGALKLARAVTG 130 Query: 125 DVYGPQKYEIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAIS 184 + +AA FHG+T ++V G+ +Y F P G+T VP+ D+EALK A+S Sbjct: 131 ------RPGFVAAEGGFHGKTFGALSVSGRQRYRAPFHPLLPGVTLVPFGDVEALKRAVS 184 Query: 185 DKTCAVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHY 244 +T AV+LEPIQGEGGV PA + YL AR++CD ALL+ DEVQ+G GR G FA Sbjct: 185 QQTAAVILEPIQGEGGVHPAPRGYLTAAREICDRAGALLILDEVQTGFGRTGMPFAAQRE 244 Query: 245 GVVPDILSSAKSLGGG-FPIGAMLTTGEIAKHL--SVGTHGTTYGGNPLASAVAEAALDV 301 GVVPD++ AK+LGGG PIG + E A+ H +T+GGNPLA+A A LD Sbjct: 245 GVVPDVMCLAKALGGGVMPIGCFIARPEAARAFWEDPLIHTSTFGGNPLAAAAGLATLDW 304 Query: 302 INTPEVLDGVKAKHERFKSRLQKIGQEY-GIFDEIRGMGLLIGAALTDEWKGKARDVLNA 360 + ++ K +++ + Y G E+RG GLL+G DE +G V++ Sbjct: 305 LQREDLPRAAAETGRWLKGEFEEMAKRYPGWIREVRGEGLLLGVEFVDEARGGL--VMSG 362 Query: 361 AEKEAVMVLQASPD--VVRFAPSLVIDDAEIDEGLERFE 397 ++ V+ + VVR PSL ID + + LE ++ Sbjct: 363 LVEKGVLTAFTLNEYRVVRVEPSLTIDRGLLIQVLEAWD 401 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: 495 Number of extensions: 30 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: 406 Length of database: 466 Length adjustment: 32 Effective length of query: 374 Effective length of database: 434 Effective search space: 162316 Effective search space used: 162316 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: 51 (24.3 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