Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_041100392.1 SUTH_RS15085 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >NCBI__GCF_000828635.1:WP_041100392.1 Length = 388 Score = 259 bits (661), Expect = 1e-73 Identities = 155/394 (39%), Positives = 212/394 (53%), Gaps = 18/394 (4%) Query: 4 SRLRPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGS 63 SRL TT+F MS LA GA+NL QGFPD P++L+ +A G NQYPP G Sbjct: 7 SRLPNVGTTIFTVMSRLAAEHGAINLSQGFPDFSPSPRLLERVTHHMAAGANQYPPMAGV 66 Query: 64 APLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYS 123 A LR AIA + R + +YDPETEV VT GAT+AI A+ V PG EV++ P YDSY Sbjct: 67 ASLREAIAEKVARLYLANYDPETEVTVTAGATQAIYTAIAACVRPGDEVIVFAPVYDSYV 126 Query: 124 PVVAMAGAHRVTVPL-VPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELA 182 P + + G H V L P+ F D D +R +TPRTR +IINSPHNP+G+V SA ++A Sbjct: 127 PGIELNGGHAVHAHLRFPE---FKPDWDEVRALITPRTRMIIINSPHNPSGSVWSAADMA 183 Query: 183 AIAEIAVAANLVVITDEVYEHLVFDH-----ARHLPLAGFDGMAERTITISSAAKMFNCT 237 + + +VV++DEVYEH+VFD RH + + G+ ER+ +SS K ++ T Sbjct: 184 MLETLVRDTKIVVVSDEVYEHVVFDQQDGGSLRHESVTRYPGLRERSFVVSSFGKTYHVT 243 Query: 238 GWKIGWACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDR 297 GWK+ + P L+ R A Q++ + P Q A+A + + L + +A+RD Sbjct: 244 GWKVAYCLAPRALMGEFRKAHQFIVFTVHHPAQLALADFMREHPEFADTLASFYQAKRDF 303 Query: 298 LAAGLTEIGFAVHDSYGTYFLCADPRPLGYDDSTEFCAALPEKVGVAAIPMSAFCDPAAG 357 L F + GTYF A + + T F L ++ GVAAIP+SAF Sbjct: 304 FRQQLEGSRFVLLPCAGTYFQLATYAAISDEPDTSFVQRLTKQHGVAAIPVSAFNPDGDD 363 Query: 358 QASQQADVWNHLVRFTFCKRDDTLDEAIRRLSVL 391 Q ++RF F K + TL A RL L Sbjct: 364 Q---------RVIRFCFAKNEATLAAAGERLRAL 388 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: 372 Number of extensions: 16 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: 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 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