Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_086509348.1 BZY95_RS07615 succinyldiaminopimelate transaminase
Query= BRENDA::Q82IK5 (364 letters) >NCBI__GCF_002151265.1:WP_086509348.1 Length = 408 Score = 142 bits (357), Expect = 2e-38 Identities = 115/356 (32%), Positives = 163/356 (45%), Gaps = 25/356 (7%) Query: 6 DRLPTFPWDKLEPYKARAAAHPD-GIVDLSVGTPVD-PVPELIQKALVAAADSPGYPTVW 63 D L +P++KL KA + L++G P P + D YP Sbjct: 6 DALKPYPFEKLATLKAGVTPPAQLAHIPLTIGEPQHAPFAGALATLHAHQLDFARYPATS 65 Query: 64 GTPELRDALTGWVERRLGARGVT-HHHVLPIVGSKELV-AWLPTQLGLGPGDKVAHPRLA 121 G PELR A+ W RR G+ VLP+ G++E + A++ L +VA P Sbjct: 66 GIPELRGAIAAWARRRFRLDGLDPERQVLPVNGTREAIFAFVQAALDRSRPARVAVPNPF 125 Query: 122 YPTYEVGARLA---------RADHVVYDD----PTELDPTGLKLLWLNSPSNPTGKVLSK 168 Y YE LA RA+ D P E+ +++L+L SP NPTG V + Sbjct: 126 YQIYEGATLLAGGQPHYLDCRAESGFRPDFDAVPAEVWRE-VQILFLCSPGNPTGAVTPR 184 Query: 169 AELTRIVAWAREHGILVFSDECYLELGWEAD--PVSVLHPDVCGG--SYEGIVSVHSLSK 224 AE +++A A E ++ SDECY EL + D P +L G Y + HSLSK Sbjct: 185 AEFQKLIALADEFDFIIASDECYSELYLDEDAPPPGLLEACAAMGRHDYRRCLVFHSLSK 244 Query: 225 RSNLAGYRAAFLAGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAALGDDAHVREQRERYAA 284 RSNL G R+ F+AGD ++ P + R + G S P Q A + A D+AHVR R+ Y Sbjct: 245 RSNLPGLRSGFVAGDAELIAPFKRYRTYHGCAMSLPLQHASITAWNDEAHVRANRDAYRE 304 Query: 285 RRTALRDALLSHGFRIEHSEASLYLW--ATRGESCWDTVAHLADLGILVAPGDFYG 338 + A+ + +L+ EAS YLW G+ T A + V PG + G Sbjct: 305 KFAAVTE-ILAPVLEFPAPEASFYLWPAVPGGDDEAFTRELFAAEHVSVLPGSYMG 359 Lambda K H 0.319 0.135 0.420 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: 444 Number of extensions: 24 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: 364 Length of database: 408 Length adjustment: 30 Effective length of query: 334 Effective length of database: 378 Effective search space: 126252 Effective search space used: 126252 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 (21.7 bits) S2: 50 (23.9 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