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 GFF2610 Psest_2661 Isopropylmalate/homocitrate/citramalate synthases
Query= CharProtDB::CH_122457 (599 letters) >FitnessBrowser__psRCH2:GFF2610 Length = 311 Score = 182 bits (461), Expect = 2e-50 Identities = 103/277 (37%), Positives = 156/277 (56%), Gaps = 6/277 (2%) Query: 6 KTVRIVEVGPRDGLQNIPQSIDSTIKLDLIRRLRDAGLQTIELTSFVSPRAIPQLADAQV 65 K + I EV RDG Q + + K+ LI RL GL IE+TSF SP+AIP L DA+ Sbjct: 3 KRLYIQEVATRDGFQIEADFVPTEAKIALIDRLSQTGLAKIEVTSFTSPKAIPNLRDAED 62 Query: 66 VVQNADIQKLLKNPKLRLPVLVPNLKGLERALHNGIKEVAVFISATEGFSRANINCTVDE 125 V++ + + + VLVPN+KG ERAL + E+ + +SA++ AN+ T ++ Sbjct: 63 VMRG-----IRRVEGVEYTVLVPNVKGCERALACEVDEINLVMSASDTHGLANLRMTPEQ 117 Query: 126 GLERARQVASRAASAGLSVRGYVSCIFADPYDGPTRPSSVLRCTKALLDAGCYEVSLGDT 185 L + R++ +G+ + +S F P++G + + LL+ G ++L DT Sbjct: 118 SLVQFREIIEVTRGSGVFINASLSTTFGCPFEGDVPERRIYELVQRLLEIGVQGITLCDT 177 Query: 186 LGIGTPADVRWLITYLQDNGVPLEMLAGHFHDTYGGAVANVWEAYKCGLRMFDSSVAGLG 245 G+ PA V I + N P + HFH+T G +AN A G+ FD+S+ GLG Sbjct: 178 TGMADPAQVE-RICHEVLNSWPQAVFTAHFHNTRGMGLANALAALNAGIDRFDASLGGLG 236 Query: 246 GCPXALGAKGNVASEDLVYMFERSGIHTGVDLSKLVE 282 GCP A GA GN+ +EDLV+MF+R G++TGVDL +L++ Sbjct: 237 GCPYAPGASGNICTEDLVHMFQRMGLNTGVDLDRLLQ 273 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: 422 Number of extensions: 24 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: 311 Length adjustment: 32 Effective length of query: 567 Effective length of database: 279 Effective search space: 158193 Effective search space used: 158193 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