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 Ac3H11_4530 Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4)
Query= CharProtDB::CH_122457 (599 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4530 Length = 306 Score = 184 bits (466), Expect = 6e-51 Identities = 121/309 (39%), Positives = 166/309 (53%), Gaps = 15/309 (4%) Query: 8 VRIVEVGPRDGLQNIPQSIDSTIKLDLIRRLRDAGLQTIELTSFVSPRAIPQLADAQVVV 67 + I EVGPRDGLQ++ ++ + KL I L AGL+ IE+ SFV R +PQ+AD VV Sbjct: 6 ILISEVGPRDGLQSVQATMPTADKLRWIDALVAAGLREIEVGSFVPARLLPQMADVAEVV 65 Query: 68 QNADIQKLLKNPKLRLPVLVPNLKGLERALHNGIKEVAVFISATEGFSRANINCTVDEGL 127 ++A L +P + + L PNL+G E AL G+ +V + +SA+ S AN+ T + + Sbjct: 66 RHA-----LTHPGITVMALAPNLRGAEAALAAGVHKVTLPVSASAAHSLANVRKTREAMV 120 Query: 128 ERARQVASR--AASAGLSVRGYVSCIFADPYDGPTRPSSVLRCTKALLDAGCYEVSLGDT 185 E R VA A + G V +S F G VL +AG EV L DT Sbjct: 121 EEVRAVAQLRDAQAPGTLVEVGLSTAFGCTLQGAVPEDDVLWLAGLCAEAGADEVGLSDT 180 Query: 186 LGIGTPADVRWLITYLQDNGVPLEMLAGHFHDTYGGAVANVWEAYKCGLRMFDSSVAGLG 245 G+ PA VR L T L+ + + A H H+T G +AN AY G+R FD+S+ GLG Sbjct: 181 TGMANPAQVRRLFTRLRAE-LGAKAGAAHMHNTRGLGLANCLAAYDVGVRTFDASLGGLG 239 Query: 246 GCPXALGAKGNVASEDLVYMFERSGIHTGVDLSKLVETGEWISRQLSIAISSRAGAALWA 305 GCP A GA GNV +EDLV+MFE GI TGVDL +L+ + L G ++ Sbjct: 240 GCPYAPGASGNVVTEDLVFMFEAMGITTGVDLERLMAARAPLQAGL-------PGEPVYG 292 Query: 306 MRKQTAVPK 314 M + +PK Sbjct: 293 MTPEAGLPK 301 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: 406 Number of extensions: 20 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: 306 Length adjustment: 32 Effective length of query: 567 Effective length of database: 274 Effective search space: 155358 Effective search space used: 155358 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