Align 3-Hydroxy-3-isohexenylglutaryl-CoA lyase (EC 4.1.3.26) (characterized)
to candidate 6937188 Sama_1358 pyruvate carboxyltransferase (RefSeq)
Query= BRENDA::Q9I2A0 (300 letters) >FitnessBrowser__SB2B:6937188 Length = 296 Score = 382 bits (980), Expect = e-111 Identities = 186/296 (62%), Positives = 236/296 (79%), Gaps = 1/296 (0%) Query: 1 MNLPKKVRLVEVGPRDGLQNEKQPIEVADKIRLVDDLSAAGLDYIEVGSFVSPKWVPQMA 60 M LP + L EVGPRDGLQNEKQ + ADKI LV+ L+AAG+ IE SFVSPKWVPQMA Sbjct: 1 MALPTHISLFEVGPRDGLQNEKQ-VTTADKILLVESLAAAGVKRIEAASFVSPKWVPQMA 59 Query: 61 GSAEVFAGIRQRPGVTYAALAPNLKGFEAALESGVKEVAVFAAASEAFSQRNINCSIKDS 120 S EV GI + GV Y+AL PNLKG E AL++ EVAVFAAASE FSQ+NINCSI++S Sbjct: 60 DSGEVLKGISRVAGVRYSALTPNLKGLELALDANASEVAVFAAASEGFSQKNINCSIEES 119 Query: 121 LERFVPVLEAARQHQVRVRGYISCVLGCPYDGDVDPRQVAWVARELQQMGCYEVSLGDTI 180 +ERF+P++E A++H + VRGY+SCVLGCPYDG++ +VA V+ L ++GCYE+SLGDTI Sbjct: 120 IERFIPLIEKAKEHNLPVRGYVSCVLGCPYDGEIATSEVARVSEILYKLGCYEISLGDTI 179 Query: 181 GVGTAGATRRLIEAVASEVPRERLAGHFHDTYGQALANIYASLLEGIAVFDSSVAGLGGC 240 GVGT R+++EAVA+ VP ++LA HFHDTYGQALANI ASL GI D+SVAGLGGC Sbjct: 180 GVGTPLKARKMVEAVAARVPVDKLALHFHDTYGQALANILASLESGIRTVDTSVAGLGGC 239 Query: 241 PYAKGATGNVASEDVLYLLNGLEIHTGVDMHALVDAGQRICAVLGKSNGSRAAKAL 296 PYAKGA+GN+ASED++Y+L+G+ I TG+D+H L++AG RI A LG+ +G++ A+AL Sbjct: 240 PYAKGASGNLASEDLVYMLHGMGIETGIDLHKLIEAGNRISAALGRHSGAKVARAL 295 Lambda K H 0.318 0.135 0.392 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: 293 Number of extensions: 11 Number of successful extensions: 2 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: 300 Length of database: 296 Length adjustment: 26 Effective length of query: 274 Effective length of database: 270 Effective search space: 73980 Effective search space used: 73980 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: 48 (23.1 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