Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate N515DRAFT_1410 N515DRAFT_1410 methionine aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >FitnessBrowser__Dyella79:N515DRAFT_1410 Length = 381 Score = 271 bits (693), Expect = 2e-77 Identities = 164/389 (42%), Positives = 218/389 (56%), Gaps = 13/389 (3%) Query: 4 SRLRPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGS 63 ++L TT+F+ MS LA AVNLGQGFPD + P + +A A+A G NQY PG G Sbjct: 5 TKLPKVGTTIFSVMSQLAVEHQAVNLGQGFPDFEPPQALREAIARAMAEGRNQYAPGIGL 64 Query: 64 APLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYS 123 LR IA + R +G D EV VT GATEA+ AA+ +V G EV++ +P YDSY Sbjct: 65 PTLREQIALKTERMYGRRIDAAGEVTVTSGATEALFAAIAAVVRAGDEVIVFDPAYDSYE 124 Query: 124 PVVAMAGAHRVTVPL-VPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELA 182 PV+ + GA V +PL VP F +D +R AVTPRTR ++INSPHNP+GAVLSA +L Sbjct: 125 PVIELQGAKAVHIPLTVPS---FGVDWQRVRDAVTPRTRMILINSPHNPSGAVLSAADLD 181 Query: 183 AIAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIG 242 +A I +VV++DEVYEH+VFD A H + +A R+I +SS K ++CTGWK+G Sbjct: 182 QLAAIVRDTEIVVLSDEVYEHIVFDGALHQSVLRHAELAARSIVVSSFGKTYHCTGWKLG 241 Query: 243 WACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGL 302 +A PA L A R QYL++ P Q A A + + L +A+RDR A + Sbjct: 242 YAVAPAALSAEFRKVHQYLTFCTFHPAQVAFAEFMASTPEHYLELPAFYQAKRDRFRALI 301 Query: 303 TEIGFAVHDSYGTYFLCADPRPLGYDDSTEFCAALPEKVGVAAIPMSAFCDPAAGQASQQ 362 F + D G YF D + + FC L ++ GVAAIP++ F + A Sbjct: 302 APSRFKLLDVPGGYFQLVDYSAIRDEPDVTFCEWLVKQGGVAAIPLAPFYETAPD----- 356 Query: 363 ADVWNHLVRFTFCKRDDTLDEAIRRLSVL 391 LVR F K D T+D A RL L Sbjct: 357 ----TRLVRLCFAKSDATMDAAAERLCKL 381 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: 397 Number of extensions: 15 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: 381 Length adjustment: 30 Effective length of query: 367 Effective length of database: 351 Effective search space: 128817 Effective search space used: 128817 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