Align 3-hydroxy-3-methylglutaryl-coenzyme A lyase/3-methylglutaconyl-coenzyme A hydratase; EC 4.1.3.4; EC 4.2.1.18 (characterized)
to candidate RR42_RS00955 RR42_RS00955 hydroxymethylglutaryl-CoA lyase
Query= CharProtDB::CH_122457 (599 letters) >FitnessBrowser__Cup4G11:RR42_RS00955 Length = 311 Score = 258 bits (658), Expect = 3e-73 Identities = 135/307 (43%), Positives = 192/307 (62%), Gaps = 9/307 (2%) Query: 8 VRIVEVGPRDGLQNIPQSIDSTIKLDLIRRLRDAGLQTIELTSFVSPRAIPQLADAQVVV 67 V++VEVGPRDGLQN + + +K+DLI RL DAG IE SFVSP+ +PQ+AD V+ Sbjct: 7 VKVVEVGPRDGLQNEKAMVPTEVKVDLINRLSDAGFVNIEAASFVSPKWVPQMADGADVM 66 Query: 68 QNADIQKLLKNPKLRLPVLVPNLKGLERALHNGIKEVAVFISATEGFSRANINCTVDEGL 127 ++ + P VL PN+KG E A+ EV +F +A+E FS+ NINC++ E + Sbjct: 67 A-----RIQRRPGTLYSVLTPNMKGFEGAVAASADEVVIFGAASEAFSQKNINCSIAESI 121 Query: 128 ERARQVASRAASAGLSVRGYVSCIFADPYDGPTRPSSVLRCTKALLDAGCYEVSLGDTLG 187 ER VA+ A GL +R +SC PY G +V+ + + D GC E+ + DT+G Sbjct: 122 ERFAPVAAAAKEKGLRLRASISCALGCPYQGEVPVHAVVDVVRRMRDLGCDEIDIADTIG 181 Query: 188 IGTPADVRWLITYLQDNGVPLEMLAGHFHDTYGGAVANVWEAYKCGLRMFDSSVAGLGGC 247 +GTP V+ ++ + P++ L+GHFHDTYG A++N+ + + G+ +F +SVAGLGGC Sbjct: 182 VGTPGRVQEVMHAVAAE-FPIDRLSGHFHDTYGQALSNILASLQVGISIFHASVAGLGGC 240 Query: 248 PXALGAKGNVASEDLVYMFERSGIHTGVDLSKLVETGEWISRQLSIAISSRAGAAL---W 304 P A GA GNVA+ED++YM GIHTGVDL ++V G++IS+ + A SSR G AL W Sbjct: 241 PYAKGATGNVATEDVLYMLHGMGIHTGVDLEQVVRAGDFISQSIGRANSSRVGRALLTKW 300 Query: 305 AMRKQTA 311 A A Sbjct: 301 AAAADAA 307 Lambda K H 0.318 0.134 0.389 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: 403 Number of extensions: 12 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: 599 Length of database: 311 Length adjustment: 32 Effective length of query: 567 Effective length of database: 279 Effective search space: 158193 Effective search space used: 158193 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 (21.7 bits) S2: 51 (24.3 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