Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate CA265_RS08140 CA265_RS08140 methionine aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >FitnessBrowser__Pedo557:CA265_RS08140 Length = 381 Score = 240 bits (613), Expect = 4e-68 Identities = 128/385 (33%), Positives = 214/385 (55%), Gaps = 12/385 (3%) Query: 4 SRLRPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGS 63 S+L +TT+F+ MS LA A+NL QGFPD PK+++ A+ G NQY P PGS Sbjct: 6 SKLPGVSTTIFSVMSKLAAEHNAINLSQGFPDYACDPKLVELVNKAMQDGFNQYAPMPGS 65 Query: 64 APLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYS 123 L+ IA + + + Y+PETE+ VT G T+AI A+ ++ G EV++ EP YDSY+ Sbjct: 66 TFLKETIAEKVENLYNIKYNPETEITVTAGGTQAIFTALASIINAGDEVIIFEPAYDSYA 125 Query: 124 PVVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELAA 183 P + + G T L P +A+D D +++ T +TR +I+N+P NPTG++LS+ ++ + Sbjct: 126 PTIKLLGGLVKTYELAPP--NYAIDWDMVKKLFTAKTRMIILNTPQNPTGSILSSDDMKS 183 Query: 184 IAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIGW 243 + ++ ++++++DEVYEHL++D +H + + + +R+ I+S K+ + TGWK+G+ Sbjct: 184 LIKLISGTDILILSDEVYEHLIYDEQKHQSVMLYPELKQRSFIIASFGKLLHATGWKLGY 243 Query: 244 ACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGLT 303 P +L R Q+ + +P Q A+A + E + + + +RD + L Sbjct: 244 CLAPEKLTKEFRKVHQFNVFSVNSPMQQAIAHYI-KEPKNYTEIGSFFQQKRDYFRSLLA 302 Query: 304 EIGFAVHDSYGTYFLCADPRPLGYDDSTEFCAALPEKVGVAAIPMSAFCDPAAGQASQQA 363 E F + G+YF C + + T+F L ++ GVA IP+SAF Q Sbjct: 303 ESRFKLLPCNGSYFQCVSYSSISDEKDTDFSMRLIKEFGVATIPVSAF---------YQK 353 Query: 364 DVWNHLVRFTFCKRDDTLDEAIRRL 388 + + ++RF F K + TL A +L Sbjct: 354 GIDHKIIRFCFAKENATLALAAEKL 378 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: 12 Number of successful extensions: 4 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