Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate BWI76_RS00585 BWI76_RS00585 dihydrodipicolinate synthase family protein
Query= BRENDA::A9CL94 (309 letters) >FitnessBrowser__Koxy:BWI76_RS00585 Length = 307 Score = 370 bits (950), Expect = e-107 Identities = 182/305 (59%), Positives = 232/305 (76%), Gaps = 1/305 (0%) Query: 3 KRIEGIIPVMITPFR-DGKIDFEGVANLVEWYIANGSDALFAVCQSSEMMFLTLEERVEL 61 K I GI+PVM+TPF D +ID+ +A L++WY+ G DALFAVCQSSEM FL+LEERVEL Sbjct: 2 KTINGIVPVMLTPFAADERIDYPALAKLIDWYLEKGVDALFAVCQSSEMQFLSLEERVEL 61 Query: 62 AAFVKRAAAGRIPVIASGHISEALEDQQKELNAIARTGVDGIVLVTNRMDARQEGGSKFL 121 A FV + GRIPVIASGHIS+ +E Q+ EL A+A+TG+D +VLVTN +D R EG F Sbjct: 62 ARFVVQRVNGRIPVIASGHISDDIEAQKAELLAMAQTGIDALVLVTNHLDPRNEGSDVFY 121 Query: 122 DDLGWLLDRLPPNLPLGLYECPAPYRRLMTDAEISFCANSGRFVILKDVSCDLETVKRRV 181 L LL+ LP +LPLGLYECPAPYRRL+TD E ++CANSGRFV+LKDVSCDL TV+RRV Sbjct: 122 AVLNTLLETLPASLPLGLYECPAPYRRLLTDDEFTWCANSGRFVVLKDVSCDLPTVERRV 181 Query: 182 ALTANTPLAIVNANAAIAFDAMKAGSRGFTGVFTNFHPDLYKWLLTEAGRKPELADELSV 241 L TPL ++NANAAIA+ A+ AGS+GF+GVFTNFHP+LY WL E + LADEL++ Sbjct: 182 RLAQGTPLNVINANAAIAWPAILAGSQGFSGVFTNFHPELYSWLWREGKNQRALADELAI 241 Query: 242 YLALAAMAEPMGYPKLAKLYHQRLGTINDIESRAVTFDIQERFWAIEPLLDKIIQGTTDF 301 +L+L A++E +GYPK AK+YHQRLGT + I R D+ ++W + +LD+I GT + Sbjct: 242 FLSLGAVSETLGYPKNAKIYHQRLGTFDSITCRVNKDDVLNKYWGLTVILDQIRAGTEQW 301 Query: 302 RQRIM 306 RQRI+ Sbjct: 302 RQRIV 306 Lambda K H 0.323 0.138 0.406 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: 304 Number of extensions: 12 Number of successful extensions: 2 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: 309 Length of database: 307 Length adjustment: 27 Effective length of query: 282 Effective length of database: 280 Effective search space: 78960 Effective search space used: 78960 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: 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