Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_057506846.1 ABB28_RS01035 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >NCBI__GCF_001431535.1:WP_057506846.1 Length = 382 Score = 276 bits (706), Expect = 7e-79 Identities = 160/389 (41%), Positives = 218/389 (56%), Gaps = 12/389 (3%) Query: 4 SRLRPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGS 63 ++L TT+F MS LA GAVNLGQGFPD P +++ A A+A G+NQYPP G Sbjct: 5 TKLPKVGTTIFTVMSQLAAEHGAVNLGQGFPDFSAPQRLIDATTAAMADGLNQYPPMTGV 64 Query: 64 APLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYS 123 APLR+AIA + +G DP+TE+ VT GATEAI A+ +V G EV++++P YD Y Sbjct: 65 APLRQAIAQKSLDLYGAQVDPDTEITVTSGATEAIFNAIHAVVRAGEEVIVLDPAYDCYE 124 Query: 124 PVVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELAA 183 P + +AGA V VPL P + FA+D D +R A+TPRTR L++N+PHNP+GA+L+ +L A Sbjct: 125 PAIDLAGARAVHVPLDP--QTFAVDWDRVRAAITPRTRLLMVNTPHNPSGAMLAEADLQA 182 Query: 184 IAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIGW 243 +A++ ++ +I+DEVYEH+++D RH + R ISS K ++CTGWKIG+ Sbjct: 183 LADLLRGTDIYLISDEVYEHIIYDGRRHESALRHPELRARAFVISSFGKTYHCTGWKIGY 242 Query: 244 ACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGLT 303 A P L A R QY ++ P Q A + E L +A+RDR L Sbjct: 243 AIAPPALSAEFRKVHQYNTFTSFGPAQYGFAAMIRDEPQHHLELGAFYQAKRDRFREQLA 302 Query: 304 EIGFAVHDSYGTYFLCADPRPLGYDDSTEFCAALPEKVGVAAIPMSAFCD-PAAGQASQQ 362 + G YF D + EF L + GVAAIP+S F + P GQ Sbjct: 303 QTRLVPLAVPGGYFQLVDYSAISDLPDHEFVKWLTIEKGVAAIPLSPFYEAPPVGQ---- 358 Query: 363 ADVWNHLVRFTFCKRDDTLDEAIRRLSVL 391 +VR F K + TLD AI RL L Sbjct: 359 -----RIVRLCFAKNEATLDAAIERLQRL 382 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: 414 Number of extensions: 18 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: 382 Length adjustment: 30 Effective length of query: 367 Effective length of database: 352 Effective search space: 129184 Effective search space used: 129184 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