Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_011885513.1 aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >NCBI__GCF_000016205.1:WP_011885513.1 Length = 390 Score = 281 bits (719), Expect = 2e-80 Identities = 164/388 (42%), Positives = 220/388 (56%), Gaps = 12/388 (3%) Query: 4 SRLRPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGS 63 SRL TT+F MSALA GAVNLGQGFPD D P+++ A A+ G NQYPP G Sbjct: 15 SRLPNVGTTIFTVMSALAAEKGAVNLGQGFPDFDCDPRIVDAVAAAMRNGHNQYPPMAGV 74 Query: 64 APLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYS 123 A LR AIA + +G YD TE+ VT GAT+A+ A+L V PG EV++IEP YDSY Sbjct: 75 ASLRDAIADKIEHLYGRRYDAATEITVTAGATQALLTAILCAVHPGDEVIVIEPTYDSYL 134 Query: 124 PVVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELAA 183 P + +AG V V L D +A+ D L A+TP+TR ++IN+PHNPTG V +L Sbjct: 135 PSIELAGGKPVFVTL--DAPDYAIPFDRLAAAITPKTRMILINTPHNPTGTVWREADLRR 192 Query: 184 IAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIGW 243 + EI N+++++DEVYEH+V+D ARH +A + +A R+ +SS K F+ TGWKIG+ Sbjct: 193 LEEIVRGTNVLILSDEVYEHMVYDGARHESVARYPELAARSFIVSSFGKTFHVTGWKIGY 252 Query: 244 ACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGLT 303 PA L A R Q+ + P Q +A L + A L + + +RD AGL Sbjct: 253 VAAPAALTAEFRKVHQFNVFTVNTPMQVGIADYL-RDPAPYLTLPDFYQKKRDFFRAGLE 311 Query: 304 EIGFAVHDSYGTYFLCADPRPLGYDDSTEFCAALPEKVGVAAIPMSAFCDPAAGQASQQA 363 F + GTYF C D + EF L ++GVAAIP+SAF A Sbjct: 312 RTRFKLLPCTGTYFQCVDYSAISDVSEAEFAKWLTAEIGVAAIPVSAF---------YHA 362 Query: 364 DVWNHLVRFTFCKRDDTLDEAIRRLSVL 391 + +VRF F K++ TL A+ RL+ L Sbjct: 363 PHESGVVRFCFAKQESTLASALERLARL 390 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: 406 Number of extensions: 19 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: 390 Length adjustment: 31 Effective length of query: 366 Effective length of database: 359 Effective search space: 131394 Effective search space used: 131394 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