Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_028314264.1 G491_RS0108285 alanine transaminase
Query= BRENDA::P9WPZ5 (397 letters) >NCBI__GCF_000429905.1:WP_028314264.1 Length = 388 Score = 155 bits (392), Expect = 2e-42 Identities = 112/356 (31%), Positives = 166/356 (46%), Gaps = 11/356 (3%) Query: 3 VSRLRPYATTVFAEMSALATRIGA--VNLGQGFPDEDGPP----KMLQAAQDAIAGGVNQ 56 + RL PY E+ A R G ++LG G PD P KM++AAQ ++ Sbjct: 7 LDRLPPYVFAQVNEIKMEARRAGEDIIDLGMGNPDLGTPQHIVDKMVEAAQKPHN---HR 63 Query: 57 YPPGPGSAPLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIE 116 Y G LR AIA +R + VD D E E +VT+GA E I+ VL + PG V Sbjct: 64 YSASMGIRKLRMAIADWYKRRYDVDIDYENEAIVTIGAKEGISHLVLVTIRPGDVVFSPS 123 Query: 117 PFYDSYSPVVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVL 176 P Y + +AG +PL PD F A R+ P+ + ++++ PHNPTG V+ Sbjct: 124 PTYPIHPFSAIIAGGDVRQIPLGPDTDFFENLITATRQT-WPKPKMMVLSFPHNPTGEVI 182 Query: 177 SATELAAIAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNC 236 I E A +++V+ D Y L +D + G + + S +K ++ Sbjct: 183 DLEFFTKIVEFAKEHDIMVVHDFAYADLTYDGYKAPSFLQAPGAKDVGVEFFSLSKSYSM 242 Query: 237 TGWKIGWACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRD 296 GW++G+ G +++A +R K YL Y P Q A +AL+ E V +R + + RRD Sbjct: 243 AGWRVGFCVGNPKIVAALRRIKSYLDYGIFQPIQIAAIIALNGEQECVEEIRQTYKMRRD 302 Query: 297 RLAAGLTEIGFAVHDSYGTYFLCAD-PRPLGYDDSTEFCAALPEKVGVAAIPMSAF 351 L GL ++G+ V GT F+ A P S EF L ++ VA P F Sbjct: 303 TLCDGLAKMGWDVPPPKGTMFVWAKIPEQYRSMGSVEFSKMLVKEAKVAVAPGLGF 358 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: 369 Number of extensions: 22 Number of successful extensions: 2 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: 388 Length adjustment: 31 Effective length of query: 366 Effective length of database: 357 Effective search space: 130662 Effective search space used: 130662 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 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