Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_085218250.1 B9N75_RS07610 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >NCBI__GCF_900177405.1:WP_085218250.1 Length = 389 Score = 158 bits (399), Expect = 3e-43 Identities = 98/308 (31%), Positives = 164/308 (53%), Gaps = 5/308 (1%) Query: 21 ATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGSAPLRRAIAAQRRRHFGV 80 A + ++L G P D P + +A + A+ G+ Y G+ R+A+A + + Sbjct: 27 AQGLDLIHLEFGRPHADTPGHIKEAVKTALDAGIVHYGDFRGTLSFRQALAEKLTDFNKL 86 Query: 81 DYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYSPVVAMAGAHRVTVPLVP 140 DY + E+LVT G T A AA + ++PG EV+L+EP+Y + V +AG VT PL Sbjct: 87 DYGVD-EILVTNGLTHASFAAFMAAIDPGDEVILLEPYYPQHVAKVELAGGTVVTAPL-D 144 Query: 141 DGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELAAIAEIAVAANLVVITDEV 200 FA+ A+ +TP+TR +++ +P NPTG V + EL +AE+A+A +L+V+ DEV Sbjct: 145 AANNFAISHAAIAAKITPKTRMIVLVNPANPTGRVYTRAELEIVAELAIAHDLIVLCDEV 204 Query: 201 YEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIGWACGPAELIAGV-RAAKQ 259 YE++ +D A H+ +A GM ERTIT + K ++ GW++G+ A LI + R Sbjct: 205 YEYITYDGAEHVSIASLPGMRERTITCFAFTKAYSMDGWRVGYLTADARLIPAILRIITT 264 Query: 260 YLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGLTEI-GFAVHDSYGTYFL 318 +++V + A A ++ + A+ + R +R+ + L ++ G + GT + Sbjct: 265 DVTHVNVFVQEGARAAVTGPQEP-MHAMVEADRRKREIVVRALNQMPGVTCAEPQGTIYA 323 Query: 319 CADPRPLG 326 D R G Sbjct: 324 FPDIRGTG 331 Lambda K H 0.321 0.135 0.405 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: 359 Number of extensions: 16 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: 397 Length of database: 389 Length adjustment: 31 Effective length of query: 366 Effective length of database: 358 Effective search space: 131028 Effective search space used: 131028 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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