Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate RR42_RS24410 RR42_RS24410 5-carboxymethyl-2-hydroxymuconate isomerase
Query= reanno::Smeli:SM_b21112 (281 letters) >FitnessBrowser__Cup4G11:RR42_RS24410 Length = 289 Score = 194 bits (492), Expect = 2e-54 Identities = 110/279 (39%), Positives = 165/279 (59%), Gaps = 10/279 (3%) Query: 9 PGQEKPGLLGSDGIIRDLSGHVSDLAAGALDPSK-----LDELANLDVETLPAV--SGNP 61 PG+ +PGL+ DGII D+S H+ + A ++ + D LA L V G Sbjct: 10 PGRPRPGLVVDDGII-DVSLHIPGVPADTVNLIENWCQWQDALARLVTRVRADVRLDGVT 68 Query: 62 RLGPCVAGTGKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPRGSEKT 121 L P V GK + IGLNY+DH AE+ P + + F K +A+ GP + +P S+ Sbjct: 69 LLAP-VPRPGKILGIGLNYADHVAESKMEPPTDQLWFAKMPTAVTGPFSAIEIPMVSDAL 127 Query: 122 DWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKSCDTFGPT 181 D+E EL +IG+ ++VS+++A ++ GYC +DVS R +Q R Q+ GKS DT P Sbjct: 128 DYEAELAFIIGRRCRHVSKSDAHKFIFGYCAANDVSVRDWQF-RTTQFLLGKSFDTHAPF 186 Query: 182 GPWLVTKDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIIST 241 GPW+VT D++ DP +L + VNGE Q +T+ +++ + +LS+ M+L PGD+I T Sbjct: 187 GPWIVTADDINDPHELPIRCFVNGELRQKSNTRNLIFNCYAQIEHLSKVMTLEPGDVIFT 246 Query: 242 GTPPGVGMGMKPPRYLKAGDVVELGIEGLGSQKQRVRAD 280 GTP GVG G KPPR L++GD V + I+G+G+ + VR + Sbjct: 247 GTPGGVGWGHKPPRPLRSGDRVRVEIDGIGAIENLVRTE 285 Lambda K H 0.315 0.136 0.408 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: 271 Number of extensions: 16 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: 281 Length of database: 289 Length adjustment: 26 Effective length of query: 255 Effective length of database: 263 Effective search space: 67065 Effective search space used: 67065 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 47 (22.7 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