Align Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4) (characterized)
to candidate Echvi_3855 Echvi_3855 Isopropylmalate/homocitrate/citramalate synthases
Query= reanno::Pedo557:CA265_RS13115 (286 letters) >FitnessBrowser__Cola:Echvi_3855 Length = 281 Score = 290 bits (742), Expect = 2e-83 Identities = 141/279 (50%), Positives = 191/279 (68%) Query: 7 KLVECPRDAMQGLHDFVPTKLKAEYLNLLLQVGFDTLDFGSFVSPKAIPQMADTAEVLAQ 66 K++ECPRDAMQG F+ T +KA Y+N LL VGFDT+DFGSFVSPKA+PQM DTAEVL Sbjct: 2 KIIECPRDAMQGREVFIDTAIKAAYINQLLNVGFDTVDFGSFVSPKAMPQMRDTAEVLDL 61 Query: 67 LDLSNTSTKLLAIVANLRGVEDAVKHQAVNYLGFPFSISETFQQRNTNSSIAQSLNTVEE 126 LDL ++ +KLLAIVAN+RG EDA++ + ++YLGFP SISETFQQRNTN SI ++L V Sbjct: 62 LDLFHSKSKLLAIVANVRGAEDAMQFEEIDYLGFPLSISETFQQRNTNKSIQEALEVVAN 121 Query: 127 MLSLCAKNNKKAVVYLSMGFGNPYGDKWNYEIVEKWADVLVSRGVEILSLADTVGISTPE 186 + ++C + V YLSMGFGNPYG+ ++ ++V ++ L GV++++L+DT+G + P Sbjct: 122 LQNMCEVKGRTLVTYLSMGFGNPYGEPFSADLVAEFVGKLDELGVKVIALSDTIGAADPA 181 Query: 187 KIENILPKLISRFSNTEIGIHLHSTPAERFEKIEAAYHSGVKRIDSALKGFGGCPMAADD 246 IE + + E G H HS EK+EA G +R D A+ GFGGCPMA D+ Sbjct: 182 LIEEVFKTNTQAYPEIEFGGHFHSRAEHIAEKVEAGLRGGCRRFDGAINGFGGCPMAKDE 241 Query: 247 LTGNIATEDVITFLNMKGEKLNLNMDKWNEAMVLSGKIF 285 L GN+ATE +I L G L +N +++ EAM L+ +F Sbjct: 242 LVGNVATEALIEVLEKNGYDLGMNQEEFGEAMKLAKFVF 280 Lambda K H 0.317 0.133 0.381 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: 284 Number of extensions: 9 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: 286 Length of database: 281 Length adjustment: 26 Effective length of query: 260 Effective length of database: 255 Effective search space: 66300 Effective search space used: 66300 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: 41 (21.7 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