Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_015798933.1 AFER_RS07925 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >NCBI__GCF_000023265.1:WP_015798933.1 Length = 398 Score = 162 bits (409), Expect = 2e-44 Identities = 125/398 (31%), Positives = 185/398 (46%), Gaps = 26/398 (6%) Query: 3 VSRLRPYATTVFAEMSA--LATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVN-QYPP 59 ++ L P AT + + +A+ I V+ G PD P +++AA A N +Y P Sbjct: 10 LTELSPSATLAIDQRAKAMVASGIDVVSFAAGEPDFPTPDFIVEAATAAARDPRNHRYTP 69 Query: 60 GPGSAPLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFY 119 G LR I +R G P + V+VT G AI A+ +VEPG EVL+ P++ Sbjct: 70 AAGLGELRELIVEVTKRDSGRVVSP-SNVVVTNGGKHAIYEAMAAIVEPGDEVLIPAPYW 128 Query: 120 DSYSPVVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSAT 179 SY +V + G V VP GF + + + A+T RT A I SP NPTGAV S Sbjct: 129 VSYPEIVRLFGGVPVAVPTTL-ANGFKVTPEQVEAAITDRTVAFIHVSPSNPTGAVYSRD 187 Query: 180 ELAAIAEIAVAANLVVITDEVYEHLVFDHARHLPLA--GFDGMAERTITISSAAKMFNCT 237 E A+AE+ A + V+TDE+Y+HL + R LA G + + R I ++ AK F T Sbjct: 188 ESRALAEVLERAGIWVLTDEIYQHLTYTGQRATSLAEVGTEALEARLIQVNGVAKTFAMT 247 Query: 238 GWKIGWACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDR 297 GW++GW PA + + V + LS Q A AL+ A +R++ RR Sbjct: 248 GWRVGWIVAPAPVASAVANLQSQLSSNVANVSQRAAIAALEAPLEATAPMRDAFARRRTT 307 Query: 298 LAAGLTEI-GFAVHDSYGTYFLCAD-----PRPLGYDDSTEFCAALPEKVGVAAIPMSAF 351 + + L I G V G +++ + + E L E+ VA +P AF Sbjct: 308 IVSALAGIEGLDVLWPDGAFYVFPSLARVLEVQMPSSSALELATRLLEEAHVAVVPGEAF 367 Query: 352 CDPAAGQASQQADVWNHLVRFTFCKRDDTLDEAIRRLS 389 P A W R ++ DD L+E +RR++ Sbjct: 368 DGPGA---------W----RLSYALGDDALEEGVRRIA 392 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: 357 Number of extensions: 18 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 397 Length of database: 398 Length adjustment: 31 Effective length of query: 366 Effective length of database: 367 Effective search space: 134322 Effective search space used: 134322 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