Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate HSERO_RS15115 HSERO_RS15115 aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >FitnessBrowser__HerbieS:HSERO_RS15115 Length = 385 Score = 279 bits (714), Expect = 9e-80 Identities = 156/389 (40%), Positives = 224/389 (57%), Gaps = 10/389 (2%) Query: 3 VSRLRPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPG 62 V++L TT+F MSALA+ GAVNLGQGFPD P ++ A A+ G+NQYPP G Sbjct: 7 VTKLPKVGTTIFTVMSALASEKGAVNLGQGFPDFHCDPALVAAVTQAMQEGLNQYPPMAG 66 Query: 63 SAPLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSY 122 LR AIA + + +G YDP +E+ VT GAT+ I +VL V PG EV++IEP YD Y Sbjct: 67 VPVLREAIAEKVEKLYGHRYDPVSEITVTAGATQGILTSVLCAVHPGDEVIVIEPVYDCY 126 Query: 123 SPVVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELA 182 P + +AG V V + +G+++ D ++ AVTP+TR +++N+PHNPTG+V+ A ++A Sbjct: 127 VPAIELAGGVPVFVQMEVGAQGYSIPWDKVKAAVTPKTRMIMVNTPHNPTGSVMRAADVA 186 Query: 183 AIAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIG 242 A+A+I ++++++DEVYEH+V+D H LA +AER+ SS K ++ TGWK+G Sbjct: 187 ALADIVRGTDILILSDEVYEHMVYDGQPHESLARHPELAERSFINSSFGKTYHVTGWKVG 246 Query: 243 WACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGL 302 + PA L A R Q+ + P Q +A A + A L + +RD GL Sbjct: 247 YVAAPAALTAEFRKVHQFNVFTVNTPVQYGLA-AYMKDPAPYLDLPAFYQHKRDLFRTGL 305 Query: 303 TEIGFAVHDSYGTYFLCADPRPLGYDDSTEFCAALPEKVGVAAIPMSAFCDPAAGQASQQ 362 F + S GTYF C + EFC L ++GVAAIP+SAF + Sbjct: 306 ANTRFELLPSQGTYFQCVKYGAISALPEAEFCKWLTSEIGVAAIPVSAFYNTPRESG--- 362 Query: 363 ADVWNHLVRFTFCKRDDTLDEAIRRLSVL 391 +VRF F K+D+TL A+ RL+ L Sbjct: 363 ------IVRFCFAKKDETLQLALERLAKL 385 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: 403 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: 385 Length adjustment: 31 Effective length of query: 366 Effective length of database: 354 Effective search space: 129564 Effective search space used: 129564 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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