Align Hydroxymethylglutaryl-CoA lyase YngG; HL; HMG-CoA lyase; 3-hydroxy-3-methylglutarate-CoA lyase; EC 4.1.3.4 (characterized)
to candidate GFF2610 Psest_2661 Isopropylmalate/homocitrate/citramalate synthases
Query= SwissProt::O34873 (299 letters) >FitnessBrowser__psRCH2:GFF2610 Length = 311 Score = 252 bits (643), Expect = 9e-72 Identities = 132/294 (44%), Positives = 185/294 (62%) Query: 5 KKVTIKEVGPRDGLQNEPVWIATEDKITWINQLSRTGLSYIEITSFVHPKWIPALRDAID 64 K++ I+EV RDG Q E ++ TE KI I++LS+TGL+ IE+TSF PK IP LRDA D Sbjct: 3 KRLYIQEVATRDGFQIEADFVPTEAKIALIDRLSQTGLAKIEVTSFTSPKAIPNLRDAED 62 Query: 65 VAKGIDREKGVTYAALVPNQRGLENALEGGINEACVFMSASETHNRKNINKSTSESLHIL 124 V +GI R +GV Y LVPN +G E AL ++E + MSAS+TH N+ + +SL Sbjct: 63 VMRGIRRVEGVEYTVLVPNVKGCERALACEVDEINLVMSASDTHGLANLRMTPEQSLVQF 122 Query: 125 KQVNNDAQKANLTTRAYLSTVFGCPYEKDVPIEQVIRLSEALFEFGISELSLGDTIGAAN 184 +++ + + + A LST FGCP+E DVP ++ L + L E G+ ++L DT G A+ Sbjct: 123 REIIEVTRGSGVFINASLSTTFGCPFEGDVPERRIYELVQRLLEIGVQGITLCDTTGMAD 182 Query: 185 PAQVETVLEALLARFPANQIALHFHDTRGTALANMVTALQMGITVFDGSAGGLGGCPYAP 244 PAQVE + +L +P HFH+TRG LAN + AL GI FD S GGLGGCPYAP Sbjct: 183 PAQVERICHEVLNSWPQAVFTAHFHNTRGMGLANALAALNAGIDRFDASLGGLGGCPYAP 242 Query: 245 GSSGNAATEDIVYMLEQMDIKTNVKLEKLLSAAKWIEEKMGKPLPSRNLQVFKS 298 G+SGN TED+V+M ++M + T V L++LL A + + +G +P L+ K+ Sbjct: 243 GASGNICTEDLVHMFQRMGLNTGVDLDRLLQCAADLPQLVGHDVPGAVLKAGKA 296 Lambda K H 0.315 0.132 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: 227 Number of extensions: 9 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: 299 Length of database: 311 Length adjustment: 27 Effective length of query: 272 Effective length of database: 284 Effective search space: 77248 Effective search space used: 77248 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 (21.6 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