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 BPHYT_RS03930 BPHYT_RS03930 3-hydroxy-3-methylglutaryl-CoA lyase
Query= CharProtDB::CH_122457 (599 letters) >FitnessBrowser__BFirm:BPHYT_RS03930 Length = 325 Score = 165 bits (418), Expect = 2e-45 Identities = 106/288 (36%), Positives = 156/288 (54%), Gaps = 14/288 (4%) Query: 1 MQNSTKTVRIVEVGPRDGLQNIPQSIDSTIKLDLIRRLRDAGLQTIELTSFVSPRAIPQL 60 M + + V + EVG RDGLQ+I +++ + K I AG++ +E+ SFV + +PQ+ Sbjct: 1 MSDIQERVVVTEVGMRDGLQSIARTMPTEFKRRWIDAAYAAGVRHMEVASFVPAKLLPQM 60 Query: 61 ADAQVVVQNADIQKLLKNPKLRLPVLVPNLKGLERALHNGIKEVAVFISATEGFSRANIN 120 ADA V+ +A L L + LVPNLKG +RAL G+ + IS + S AN+ Sbjct: 61 ADADEVIAHA-----LTYDDLMVTALVPNLKGAQRALEAGVHRIVAPISVSSAHSLANVR 115 Query: 121 CTVDEGLERARQV------ASRAASAGLSVRGYVSCIFADPYDGPTRPSSVLRCTKALLD 174 T E +E + S+A + + +S +F G + + +A + Sbjct: 116 RTPAEMIEAFAAMRESIDGTSKAGGRRVELIAGLSTVFGCTLQGAVPYADIAAIARAAVQ 175 Query: 175 AGCYEVSLGDTLGIGTPADVRWLITYLQDN-GVPLEMLAGHFHDTYGGAVANVWEAYKCG 233 AG ++LGDT G TP V +I ++D G L L HFHDT G +AN A + G Sbjct: 176 AGADVIALGDTTGEATPRQVGEIIELVRDVVGGKLHSL--HFHDTRGLGLANTLVALQHG 233 Query: 234 LRMFDSSVAGLGGCPXALGAKGNVASEDLVYMFERSGIHTGVDLSKLV 281 +R FD+S+AGLGGCP A GA GNV +EDLV+M + G TG+DL +L+ Sbjct: 234 IREFDASLAGLGGCPHAPGATGNVNTEDLVFMLDSMGYETGIDLDRLL 281 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: 392 Number of extensions: 22 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: 325 Length adjustment: 32 Effective length of query: 567 Effective length of database: 293 Effective search space: 166131 Effective search space used: 166131 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