Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate SM_b20259 SM_b20259 dihydrodipicolinate synthase
Query= BRENDA::A9CGZ4 (321 letters) >FitnessBrowser__Smeli:SM_b20259 Length = 320 Score = 566 bits (1458), Expect = e-166 Identities = 283/320 (88%), Positives = 298/320 (93%) Query: 1 MTASIFSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQR 60 M A IFSGVIPALMTP R+DRTPDFDALVRKGK LIADGMSAVVYCGSMGDWPLLTD QR Sbjct: 1 MKAKIFSGVIPALMTPGREDRTPDFDALVRKGKALIADGMSAVVYCGSMGDWPLLTDAQR 60 Query: 61 MEGVERLVKAGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGSVIAAQKAH 120 MEGVERLVKAG+PVIVGTGAVNTA A AHA HAQKVGA+GLMVIPRVLSRG I AQKAH Sbjct: 61 MEGVERLVKAGVPVIVGTGAVNTALAAAHAAHAQKVGAQGLMVIPRVLSRGPSIVAQKAH 120 Query: 121 FKAILSAAPEIPAVIYNSPYYGFATRADLFFALRAEHKNLVGFKEFGGPADMRYAAENIT 180 FKAIL+AAP++P+VIYNSPYYGFATRADLFFALRAEH NLVGFKEFGG ADMRYAAE+IT Sbjct: 121 FKAILAAAPDLPSVIYNSPYYGFATRADLFFALRAEHPNLVGFKEFGGNADMRYAAEHIT 180 Query: 181 SRDDEVTLMIGVDTAVVHGFVNCGATGAITGIGNVLPKEVIHLCKLSQAAAKGDADARAR 240 SRDD V+LMIGVDTAV HGFVNCGATGAITGIGNVLPKEVIHLC LS+AAA GD DAR R Sbjct: 181 SRDDGVSLMIGVDTAVFHGFVNCGATGAITGIGNVLPKEVIHLCNLSRAAAAGDVDARQR 240 Query: 241 ALELEQALAVLSSFDEGPDLVLYFKYMMVLKGDKEYTLHFNETDALTDSQRGYVEAQFKL 300 A ELEQALAVLSSFDEGPDLVLYFK+MMVLKGDKEYTLHFNETDALT+SQRGYVEAQFKL Sbjct: 241 AQELEQALAVLSSFDEGPDLVLYFKHMMVLKGDKEYTLHFNETDALTESQRGYVEAQFKL 300 Query: 301 FNSWYADWSKLPGAVQTCKA 320 FN+WYA+WSKLPGAV+ KA Sbjct: 301 FNTWYAEWSKLPGAVEKYKA 320 Lambda K H 0.320 0.135 0.398 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: 451 Number of extensions: 10 Number of successful extensions: 1 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: 321 Length of database: 320 Length adjustment: 28 Effective length of query: 293 Effective length of database: 292 Effective search space: 85556 Effective search space used: 85556 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 (21.8 bits) S2: 48 (23.1 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