Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_092350282.1 BLU87_RS15000 aspartate aminotransferase family protein
Query= reanno::WCS417:GFF4238 (406 letters) >NCBI__GCF_900107645.1:WP_092350282.1 Length = 463 Score = 162 bits (411), Expect = 1e-44 Identities = 121/396 (30%), Positives = 194/396 (48%), Gaps = 45/396 (11%) Query: 30 RGEGSRVWDQAGRELIDFAGGIAVNVLGHAHPALVGALTEQAHKLWHVSNVFTNEPALRL 89 R GS ++D G+ +DF G + V G+ HP +V A+TE+ +L FTN PA+ L Sbjct: 60 RSHGSYLFDTNGKSYLDFHGNSSHQV-GYGHPHVVAAITEEMQRLPFSPRRFTNRPAVEL 118 Query: 90 AHKLIDATFAE--RVFFCNSGAEANEAAFKLARRVAFDRFGSEKYEIIAALNSFHGRTLF 147 A KL + R+ F G AN A KLAR V + +++ ++ ++FHG +L Sbjct: 119 AKKLAQLSPGNLNRMLFAPGGTSANGIALKLARSV------TGRFKTLSFWDAFHGASLD 172 Query: 148 TVNVGGQSKYSDGFGPKITGITHVP--------YNDLDALKA--------AVSDKTCAVV 191 ++VGG++ + GP + G VP + LD KA A + Sbjct: 173 AISVGGEALFRRNMGPLLPGCIQVPAPGSHCFGVDKLDWQKALGYIEYVMVHEGDVAAFI 232 Query: 192 LEPIQGEGGVLPAELAYLQGARDLCDANNALLVFDEVQTGMGRSGHLFAYQHYGVTPDIL 251 EP++ +P + + + R++CD + LL+FDE+ +GR+G +FA ++Y V PDIL Sbjct: 233 AEPMRCTTIDIPP-VQFWRQIREICDRHGVLLIFDEIPLCLGRTGFMFACEYYAVVPDIL 291 Query: 252 TSAKSLGGG-FPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLAG 310 K LGGG FP+AA L E L T+ +P+ CA A A ++VI +L Sbjct: 292 CLGKGLGGGIFPMAATLIREDLEIDPAQALGHYTHEKSPVGCAAALATLEVIADEHLLQR 351 Query: 311 VN--AKHDLFKARLEQIGKQYGIFTEVRGMGLLLG----------CVLSDAFKGKAKDVF 358 +H L A L ++ ++ + + VRG+GL+LG C +DA A+ + Sbjct: 352 SRELGRHTL--AALHRLRSEHPLISAVRGVGLMLGIEITPPAGFTCSATDA----AEQIL 405 Query: 359 NAAEKENLMILQAGPDVVRFAPSLVVEDADIKEGLD 394 AA + L + +V+ P L + DA++ L+ Sbjct: 406 YAAFTQGLSFKISAGNVLTLTPPLTISDAEMDAALN 441 Lambda K H 0.320 0.137 0.400 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: 426 Number of extensions: 22 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: 463 Length adjustment: 32 Effective length of query: 374 Effective length of database: 431 Effective search space: 161194 Effective search space used: 161194 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: 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