Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_043743334.1 AMB_RS03565 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >NCBI__GCF_000009985.1:WP_043743334.1 Length = 386 Score = 313 bits (801), Expect = 7e-90 Identities = 174/379 (45%), Positives = 228/379 (60%), Gaps = 12/379 (3%) Query: 11 TTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGSAPLRRAI 70 TT+F MS LA GAVNLGQGFP+ P ++ A +A+ G NQYP G+ LR+AI Sbjct: 13 TTIFETMSRLAQAHGAVNLGQGFPEGLEPADVVARAAEALVAGPNQYPSMMGTPDLRQAI 72 Query: 71 AAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYSPVVAMAG 130 A RR +G + DP EV+VT GATEA+A + GL+EPG EV+LIEP YDSY P++ AG Sbjct: 73 ARHERRFYGTELDPMAEVMVTSGATEALADCLFGLIEPGDEVVLIEPLYDSYLPIIRRAG 132 Query: 131 AHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELAAIAEIAVA 190 V + P + L + L A +PRT+ +I+N+P NP+G V S E+A +A + Sbjct: 133 GIPKLVRVEPPH--WDLPRETLAAAFSPRTKLMILNTPMNPSGKVWSRDEMAFVAGLLER 190 Query: 191 ANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIGWACGPAEL 250 + + DEVYEHLV+D RHLPL GM ER + I SA K+F+ TGWK+GW +L Sbjct: 191 FDAYCVCDEVYEHLVYDGRRHLPLMTLPGMRERCLKIGSAGKIFSLTGWKVGWVVAAPDL 250 Query: 251 IAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGLTEIGFAVH 310 +A + QYL++ Q AVA LD ED++ L L RRDRLA GL +GF V Sbjct: 251 LAPLAKVHQYLTFATPPNLQSAVAWGLDKEDSYYDGLAAMLAERRDRLAEGLRGVGFEVM 310 Query: 311 DSYGTYFLCADPRPLGY-DDSTEFCAALPEKVGVAAIPMSAFCDPAAGQASQQADVWNHL 369 + G+YFL AD RPLG+ D +FC + EK GVAAIP+S F Q DV +H Sbjct: 311 AAGGSYFLTADFRPLGFAGDDDDFCRHITEKAGVAAIPISTF--------YQGGDV-DHF 361 Query: 370 VRFTFCKRDDTLDEAIRRL 388 RF F K + +DEA+ RL Sbjct: 362 ARFCFAKTESAIDEAVMRL 380 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: 467 Number of extensions: 27 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: 397 Length of database: 386 Length adjustment: 31 Effective length of query: 366 Effective length of database: 355 Effective search space: 129930 Effective search space used: 129930 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 Apr 09 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