Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate PP_0858 PP_0858 putative methionine/glutamine aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >FitnessBrowser__Putida:PP_0858 Length = 382 Score = 243 bits (620), Expect = 7e-69 Identities = 147/392 (37%), Positives = 210/392 (53%), Gaps = 11/392 (2%) Query: 1 MTVSRLRPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPG 60 M S+L TT+F MS LA + GA+NL QGFPD +GP +L A +A G NQY P Sbjct: 1 MIRSKLPNVGTTIFTTMSQLAVQTGALNLSQGFPDFNGPQALLDAVGRHVAAGHNQYSPM 60 Query: 61 PGSAPLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYD 120 G LR+ +AA+ R +G D + EV +T GATEAI A+ +V G EV++ +P YD Sbjct: 61 TGLPALRQQVAAKVERLYGARVDADQEVTITPGATEAIFCAIQAVVHAGDEVIVFDPCYD 120 Query: 121 SYSPVVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATE 180 SY P V +AG V V L DG F +D A++PRTR +I+NSPHNP+GA+++ + Sbjct: 121 SYEPSVELAGGRCVHVQL-SDG-DFRIDWQKFSDALSPRTRMVILNSPHNPSGALITRED 178 Query: 181 LAAIAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWK 240 L +A + ++ +++DEVYEHLV+D RH + + + R +SS K ++ TGWK Sbjct: 179 LDQLAALIADRDIYLVSDEVYEHLVYDGVRHASVLAHEQLYSRAFVVSSFGKTYHVTGWK 238 Query: 241 IGWACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAA 300 G+ P L A +R QY+++ G P Q A+A + + L +A+RD Sbjct: 239 TGYVIAPPALSAELRKVHQYVNFCGVTPLQCALADFMAGHPEHIDELPAFYQAKRDLFCG 298 Query: 301 GLTEIGFAVHDSYGTYFLCADPRPLGYD-DSTEFCAALPEKVGVAAIPMSAFCDPAAGQA 359 L F + GTYF D + D + + L + GVA IP+S F Sbjct: 299 LLDGSRFNFTRTTGTYFQLVDYSQIRPDLNDVDMSLWLTREHGVATIPVSVF-------- 350 Query: 360 SQQADVWNHLVRFTFCKRDDTLDEAIRRLSVL 391 QQ LVR F KR++TL +A RL + Sbjct: 351 YQQPIPEQRLVRLCFAKREETLRQAAERLCAI 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: 356 Number of extensions: 19 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 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