Align hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4) (characterized)
to candidate Dsui_0984 Dsui_0984 isopropylmalate/homocitrate/citramalate synthase
Query= BRENDA::P97519 (325 letters) >FitnessBrowser__PS:Dsui_0984 Length = 302 Score = 402 bits (1034), Expect = e-117 Identities = 195/293 (66%), Positives = 239/293 (81%) Query: 29 LPKRVKIVEVGPRDGLQNEKSIVPTPVKIKLIDMLSEAGLPVIEATSFVSPKWVPQMADH 88 LP VKIVEVGPRDGLQNEK +VPT VKI+LI+ L+ AGLP +EATSFVSPKWVPQM D+ Sbjct: 3 LPTHVKIVEVGPRDGLQNEKQVVPTAVKIELIERLAAAGLPAVEATSFVSPKWVPQMGDN 62 Query: 89 SDVLKGIQKFPGINYPVLTPNMKGFEEAVAAGAKEVSIFGAASELFTRKNVNCSIEESFQ 148 S+VL+GI++ PG+ YPVLTPN+KGF+ AV AGA EV+IFGAASE F++KN+NCSI ES + Sbjct: 63 SEVLRGIRQQPGVAYPVLTPNLKGFDSAVEAGATEVAIFGAASEAFSQKNINCSIAESLK 122 Query: 149 RFDGVMQAARAASISVRGYVSCALGCPYEGKVSPAKVAEVAKKLYSMGCYEISLGDTIGV 208 RF+ ++ AA A I VRGYVSC +GCPYEG V+P K AEVAK LY MGCYE+SLGDTIGV Sbjct: 123 RFEPIVSAASALEIKVRGYVSCVVGCPYEGAVAPEKAAEVAKILYDMGCYEVSLGDTIGV 182 Query: 209 GTPGLMKDMLTAVLHEVPVAALAVHCHDTYGQALANTLVALQMGVSVVDSSVAGLGGCPY 268 G P + +L A VP+A LA H HDTYG A+AN +LQ+G++V D+SVAGLGGCPY Sbjct: 183 GNPASVSRLLEACARHVPMAKLAGHYHDTYGMAVANIYASLQLGLAVFDASVAGLGGCPY 242 Query: 269 AKGASGNLATEDLVYMLTGLGIHTGVNLQKLLEAGDFICQALNRKTSSKVAQA 321 AKGASGN+ATED+VY+L GLGI TG++LQ+L+EAG FI L R+++SK A+A Sbjct: 243 AKGASGNVATEDVVYLLEGLGISTGIDLQRLVEAGAFISAHLGRESASKAARA 295 Lambda K H 0.318 0.133 0.381 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: 330 Number of extensions: 14 Number of successful extensions: 1 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: 325 Length of database: 302 Length adjustment: 27 Effective length of query: 298 Effective length of database: 275 Effective search space: 81950 Effective search space used: 81950 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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