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 7024490 Shewana3_1668 hydroxymethylglutaryl-CoA lyase (RefSeq)
Query= CharProtDB::CH_122457 (599 letters) >FitnessBrowser__ANA3:7024490 Length = 310 Score = 259 bits (663), Expect = 9e-74 Identities = 139/300 (46%), Positives = 194/300 (64%), Gaps = 7/300 (2%) Query: 4 STKTVRIVEVGPRDGLQNIPQSIDSTIKLDLIRRLRDAGLQTIELTSFVSPRAIPQLADA 63 S+ V + E+GPRDGLQN ++ + K+ LI L DAG++ IE SFVSP+ +PQ+AD+ Sbjct: 12 SSDRVSLFEMGPRDGLQN-EAAVPTQAKVALIESLADAGVKRIEAGSFVSPKWVPQMADS 70 Query: 64 QVVVQNADIQKLLKNPKLRLPVLVPNLKGLERALHNGIKEVAVFISATEGFSRANINCTV 123 V ++++ + + L PN+KGLE AL EVA+F +A++ FS+ NINC++ Sbjct: 71 GDV-----LRQIRRQAGVVYSALTPNVKGLELALDAKASEVAIFGAASQSFSQRNINCSI 125 Query: 124 DEGLERARQVASRAASAGLSVRGYVSCIFADPYDGPTRPSSVLRCTKALLDAGCYEVSLG 183 +E +ER + A +A + VRGYVSC+ PY+G S V R ++ L GCYE+SLG Sbjct: 126 EESIERFIPLMDMAKAANIPVRGYVSCVLGCPYEGEIAASEVARVSEILYKMGCYEISLG 185 Query: 184 DTLGIGTPADVRWLITYLQDNGVPLEMLAGHFHDTYGGAVANVWEAYKCGLRMFDSSVAG 243 DT+G+GTP R ++ + + VP+EMLA HFHDTYG A+AN+ G+R FD+SVAG Sbjct: 186 DTIGVGTPLKARKMLQAVMER-VPVEMLALHFHDTYGQALANITACLDLGVRSFDASVAG 244 Query: 244 LGGCPXALGAKGNVASEDLVYMFERSGIHTGVDLSKLVETGEWISRQLSIAISSRAGAAL 303 LGGCP A GA GN+ASEDLVYM G+ TG+DL KL G IS+QL+ S+ A+ Sbjct: 245 LGGCPYAKGASGNLASEDLVYMLHGLGLKTGIDLEKLALAGFGISKQLNRLNGSKVANAI 304 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: 407 Number of extensions: 18 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: 310 Length adjustment: 32 Effective length of query: 567 Effective length of database: 278 Effective search space: 157626 Effective search space used: 157626 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