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 HSERO_RS23475 HSERO_RS23475 hydroxymethylglutaryl-CoA lyase
Query= CharProtDB::CH_122457 (599 letters) >FitnessBrowser__HerbieS:HSERO_RS23475 Length = 302 Score = 252 bits (643), Expect = 2e-71 Identities = 134/306 (43%), Positives = 193/306 (63%), Gaps = 8/306 (2%) Query: 3 NSTKTVRIVEVGPRDGLQNIPQSIDSTIKLDLIRRLRDAGLQTIELTSFVSPRAIPQLAD 62 N K V+IVEVGPRDGLQN +I + +K++L+ RL AG +E SFVSP+ +PQ+A Sbjct: 2 NLPKKVKIVEVGPRDGLQNEKDTISAEVKIELVNRLAAAGFPNVEAASFVSPKWVPQMAT 61 Query: 63 AQVVVQNADIQKLLKNPKLRLPVLVPNLKGLERALHNGIKEVAVFISATEGFSRANINCT 122 + V+ + + P + LVPN+KG E AL G+ EV +F +A+E FS+ NINC+ Sbjct: 62 SAEVMHG-----ITRRPGVVYSALVPNMKGFEAALEAGVDEVVIFGAASEAFSQKNINCS 116 Query: 123 VDEGLERARQVASRAASAGLSVRGYVSCIFADPYDGPTRPSSVLRCTKALLDAGCYEVSL 182 + E ++R +VA A +R VSC F PY G +V + + GC E+ + Sbjct: 117 IAESIDRFAEVARAAKEHRKRLRAAVSCAFGCPYQGEVPLEAVADVVRRFRELGCDEIDI 176 Query: 183 GDTLGIGTPADVRWLI-TYLQDNGVPLEMLAGHFHDTYGGAVANVWEAYKCGLRMFDSSV 241 DT+G+ TP VR ++ T +++ +E L+GHFHDTYG A+AN++ + + G+ ++ +SV Sbjct: 177 ADTIGVATPGKVRPVMETAIRE--FHIEGLSGHFHDTYGQALANIYASLQTGISIYHASV 234 Query: 242 AGLGGCPXALGAKGNVASEDLVYMFERSGIHTGVDLSKLVETGEWISRQLSIAISSRAGA 301 AGLGGCP A GA GNVA+ED++YM GI TGVDL +VE G++IS+QL SRAG Sbjct: 235 AGLGGCPYAKGATGNVATEDVLYMMNGLGIETGVDLDAVVEAGQFISQQLGRRSVSRAGN 294 Query: 302 ALWAMR 307 A+ A R Sbjct: 295 AIAAKR 300 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: 404 Number of extensions: 13 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: 599 Length of database: 302 Length adjustment: 32 Effective length of query: 567 Effective length of database: 270 Effective search space: 153090 Effective search space used: 153090 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: 50 (23.9 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