Align Hydroxymethylglutaryl-CoA lyase YngG; HL; HMG-CoA lyase; 3-hydroxy-3-methylglutarate-CoA lyase; EC 4.1.3.4 (characterized)
to candidate Ac3H11_4530 Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4)
Query= SwissProt::O34873 (299 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4530 Length = 306 Score = 217 bits (553), Expect = 2e-61 Identities = 117/275 (42%), Positives = 157/275 (57%), Gaps = 2/275 (0%) Query: 4 PKKVTIKEVGPRDGLQNEPVWIATEDKITWINQLSRTGLSYIEITSFVHPKWIPALRDAI 63 P ++ I EVGPRDGLQ+ + T DK+ WI+ L GL IE+ SFV + +P + D Sbjct: 3 PPEILISEVGPRDGLQSVQATMPTADKLRWIDALVAAGLREIEVGSFVPARLLPQMADVA 62 Query: 64 DVAKGIDREKGVTYAALVPNQRGLENALEGGINEACVFMSASETHNRKNINKSTSESLHI 123 +V + G+T AL PN RG E AL G+++ + +SAS H+ N+ K+ + Sbjct: 63 EVVRHALTHPGITVMALAPNLRGAEAALAAGVHKVTLPVSASAAHSLANVRKTREAMVEE 122 Query: 124 LKQVNN--DAQKANLTTRAYLSTVFGCPYEKDVPIEQVIRLSEALFEFGISELSLGDTIG 181 ++ V DAQ LST FGC + VP + V+ L+ E G E+ L DT G Sbjct: 123 VRAVAQLRDAQAPGTLVEVGLSTAFGCTLQGAVPEDDVLWLAGLCAEAGADEVGLSDTTG 182 Query: 182 AANPAQVETVLEALLARFPANQIALHFHDTRGTALANMVTALQMGITVFDGSAGGLGGCP 241 ANPAQV + L A A A H H+TRG LAN + A +G+ FD S GGLGGCP Sbjct: 183 MANPAQVRRLFTRLRAELGAKAGAAHMHNTRGLGLANCLAAYDVGVRTFDASLGGLGGCP 242 Query: 242 YAPGSSGNAATEDIVYMLEQMDIKTNVKLEKLLSA 276 YAPG+SGN TED+V+M E M I T V LE+L++A Sbjct: 243 YAPGASGNVVTEDLVFMFEAMGITTGVDLERLMAA 277 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: 228 Number of extensions: 5 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: 299 Length of database: 306 Length adjustment: 27 Effective length of query: 272 Effective length of database: 279 Effective search space: 75888 Effective search space used: 75888 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