Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_089322761.1 CHB58_RS03675 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >NCBI__GCF_900188395.1:WP_089322761.1 Length = 396 Score = 166 bits (419), Expect = 1e-45 Identities = 111/341 (32%), Positives = 176/341 (51%), Gaps = 10/341 (2%) Query: 21 ATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGSAPLRRAIAAQRRRHFGV 80 A I + G G PD D P + +AA AI G +Y P G LR IA + R G+ Sbjct: 28 AKGIDVIGFGAGEPDFDTPSHVKEAAIKAIEEGFTKYTPAAGIPELREVIAQKLLRENGI 87 Query: 81 DYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYSPVVAMAGAHRVTVPLVP 140 +Y ++++VT GA A+ + +L +++ G EV++ P++ +Y V AG V V Sbjct: 88 EYS-SSQIVVTDGAKFALFSLMLSVIDEGDEVIIPAPYWVTYPEQVKFAGGKPVFVN-TS 145 Query: 141 DGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELAAIAEIAVAANLVVITDEV 200 + GF + L + VT RT+ LI+ SP NPTGAV+ EL I E +++ +DE Sbjct: 146 EENGFIFTLELLEKVVTERTKLLILCSPSNPTGAVIPEDELKRIGEFCAEKGILIASDEC 205 Query: 201 YEHLVFDHARHLPLAGF-DGMAERTITISSAAKMFNCTGWKIGWACGPAELIAG-VRAAK 258 YE LV++ +H+ +A D + E TITI++ +K ++ TGW++G+A GP+E+I+ ++ Sbjct: 206 YEKLVYEGEKHVSIASISDELKEITITINALSKAYSMTGWRVGYAAGPSEIISSMIKINS 265 Query: 259 QYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGLTEI-GFAVHDSYGTYF 317 Q +S V + AVA AL ++ + RR + I G + G ++ Sbjct: 266 QSVSNVNSIAQKAAVA-ALTGPQEFLKDWLKAFDERRRYMVERFNSIPGVSCTVPKGAFY 324 Query: 318 LCADPRPL----GYDDSTEFCAALPEKVGVAAIPMSAFCDP 354 + + + G+ D EF L E VAA+P SAF P Sbjct: 325 AFPNIKKVLERGGFKDDFEFADFLIENAKVAAVPGSAFGYP 365 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: 334 Number of extensions: 21 Number of successful extensions: 6 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: 396 Length adjustment: 31 Effective length of query: 366 Effective length of database: 365 Effective search space: 133590 Effective search space used: 133590 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