Align Probable 5-dehydro-4-deoxyglucarate dehydratase 2; EC 4.2.1.41; 5-keto-4-deoxy-glucarate dehydratase 2; KDGDH 2 (uncharacterized)
to candidate CCNA_01253 CCNA_01253 dihydrodipicolinate synthase
Query= curated2:Q9RDE8 (322 letters) >FitnessBrowser__Caulo:CCNA_01253 Length = 294 Score = 105 bits (262), Expect = 1e-27 Identities = 67/213 (31%), Positives = 107/213 (50%), Gaps = 7/213 (3%) Query: 40 DGSFDADGYRAYVAERLAAGPGALFPACGTGEFFSLDEDEYRQAVAIAVEETAGSVPVVA 99 DG D + A V ++A G L P TGE +L +E+R+ V + V+ TAG VPV+A Sbjct: 19 DGEVDEKAFVALVERQIAGGVHGLVPVGTTGETSTLSHEEHRRVVELCVKTTAGRVPVIA 78 Query: 100 GTGYGWA-QALRFARIAEDAGADALLVMPHYLTAAPQDGLVAQMERIAAGTRLPLIAYQ- 157 G G +A+ AR A+ GADA LV+ Y Q+G+ + I LP+ Y Sbjct: 79 GAGSNSTDEAIELARHAKTVGADACLVVTPYYNRPSQEGMYQHYKAINDAVELPIFVYNV 138 Query: 158 --RGQVAYTAESVRRLTRVPGVIGLKDGHSDLDRLQRAVLAAPDDFLFFNGAATAEVQAR 215 R V + +++ RL ++P ++G+KD DL R+ L +++ +G + Sbjct: 139 PGRTGVDISNDTLERLAKLPNIVGIKDATGDLTRISFQRLMCGPEWVMLSGDDPTALGYM 198 Query: 216 AYAAVGVPAYSSAVHAFAPEIANAFLAALRGGD 248 A+ GV + +S V AP+ +AF+ A G+ Sbjct: 199 AHGGHGVISVTSNV---APDACSAFMNACMQGE 228 Lambda K H 0.320 0.136 0.395 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: 233 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: 322 Length of database: 294 Length adjustment: 27 Effective length of query: 295 Effective length of database: 267 Effective search space: 78765 Effective search space used: 78765 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 Sep 17 2021. The underlying query database was built on Sep 17 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