Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_090443176.1 BLS63_RS09340 succinyldiaminopimelate transaminase
Query= BRENDA::Q82IK5 (364 letters) >NCBI__GCF_900100495.1:WP_090443176.1 Length = 402 Score = 133 bits (334), Expect = 9e-36 Identities = 120/397 (30%), Positives = 179/397 (45%), Gaps = 36/397 (9%) Query: 1 MSAVSDRLPTFPWDKLEPYKARAAAHPDG-IVDLSVGTPVDPVPELIQKALVAAADSPG- 58 M+ ++L +P++KL A A + + LS+G P P + +AL A D Sbjct: 1 MNDALNQLQPYPFEKLRALLAGAQPPSEKKAIALSIGEPKHRSPAFVAEALSANLDQLAV 60 Query: 59 YPTVWGTPELRDALTGWVERRLGARGV---THHHVLPIVGSKELVAWLPTQLGLGPGDKV 115 YPT G P LR+A+ W RR G HVLP+ G++E + + TQ + D Sbjct: 61 YPTTLGIPALREAIAAWCGRRFGVPAGWLDPARHVLPVNGTREAL-FAFTQAVVNRVDSS 119 Query: 116 AHPRLA------YPTYEVGARLARAD-HVV-------YDDPTELDPTGL----KLLWLNS 157 P L Y YE A LA A H + ++ + P+ + +LL+L S Sbjct: 120 QEPGLVVSPNPFYQIYEGAALLAGAQPHYLACLQEHGFNPDFDAVPSEIWRRCQLLFLCS 179 Query: 158 PSNPTGKVLSKAELTRIVAWAREHGILVFSDECYLELGWEAD--PVSVLHP--DVCGGSY 213 P NPTG ++ L +++ A E ++ +DECY EL ++ P +L ++ + Sbjct: 180 PGNPTGALIPLETLKKLIQLADEFDFVIAADECYSELYFDEQQPPAGLLSACAELGRSDF 239 Query: 214 EGIVSVHSLSKRSNLAGYRAAFLAGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAALGDDA 273 V HSLSKRSNL G R+ F+AGD +L L R + G TQ A VAA D+ Sbjct: 240 ARCVVFHSLSKRSNLPGLRSGFVAGDADILKSFLLYRTYHGCAMPVQTQLASVAAWNDEE 299 Query: 274 HVREQRERYAARRTALRDALLSHGFRIEHSEASLYLWA-TRGESCWDTVAHLADLGILVA 332 HVR R Y + A+ D +L ++ + YLWA T + + A + V Sbjct: 300 HVRANRALYREKFAAVLD-ILGGVLDVQRPDGGFYLWAKTPVDDETFSRELFAREHVTVV 358 Query: 333 PGDFYG------SAGEQFVRVALTATDERVAAAVRRL 363 PG + + G VR+AL A A R+ Sbjct: 359 PGSYLSRSVDGLNPGANRVRMALVAPLAECVEAAERI 395 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: 424 Number of extensions: 32 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: 402 Length adjustment: 30 Effective length of query: 334 Effective length of database: 372 Effective search space: 124248 Effective search space used: 124248 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