Align dihydrodipicolinate synthase subunit (EC 4.3.3.7) (characterized)
to candidate WP_052309071.1 SACCYDRAFT_RS05540 5-dehydro-4-deoxyglucarate dehydratase
Query= metacyc::MONOMER-6565 (289 letters) >NCBI__GCF_000244975.1:WP_052309071.1 Length = 297 Score = 124 bits (310), Expect = 3e-33 Identities = 86/282 (30%), Positives = 140/282 (49%), Gaps = 10/282 (3%) Query: 11 VTPFDKNENIDFQKLSKLIDYLLNNGTDSLVVAGTTGESPTLSEEEKVALIQYSVKEAAG 70 +TPFD +D I + G +L TGE +L+E+E L+ +V+EA G Sbjct: 10 LTPFDDEGAVDLDAFRDHIRAQVAAGPGALFPCCGTGEFFSLAEDEYETLVAAAVEEAKG 69 Query: 71 RAPIIAGTGSNNTKASIKLTKKAEEAGADAVMLVTPYYNKPSQEGMYRHFRAIAEETSLP 130 R P++AG G +A+ + AE AGADA +L+ PY Q G+ H R +A T+LP Sbjct: 70 RLPVVAGVGYGWAQAA-RFAAAAERAGADAALLLPPYLVDGPQPGLVEHVRKVATSTALP 128 Query: 131 VMLYNVPGRTAASLAPETTIRLAEIPNIIAIKEASGDLDAITKIVAETPEDFAVYSGDDS 190 +++Y R ++ LAEIP++I +K+ DLD + ++ P+D+ ++G + Sbjct: 129 LIVYQ---RAQVKISTAAVAELAEIPSVIGVKDGHSDLDQVQRMKLAAPDDWLFFNGAAT 185 Query: 191 LTLPALSVGARGI--VSVASHIIGPEMQEMIKH--YTEGNTAQAALIHQKLLPL--MKGL 244 L A + A G+ S A H PE+ + + + + L+ LPL ++ Sbjct: 186 AELQARAYRAIGVPAYSSAVHAFAPEISQAFFRALHADDHAEVERLLSGFYLPLVELRDQ 245 Query: 245 FAAPNPSPLKTALQLKGLDVGSVRLPLIPLNEDERLRLSSLM 286 S +K A +L+G VGSVR PL ++ RL +L+ Sbjct: 246 GKGYAVSLVKAAARLRGHKVGSVRAPLSDPPQEHLDRLEALL 287 Lambda K H 0.313 0.131 0.357 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: 181 Number of extensions: 10 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: 289 Length of database: 297 Length adjustment: 26 Effective length of query: 263 Effective length of database: 271 Effective search space: 71273 Effective search space used: 71273 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 10 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