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 Ac3H11_199 Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4)
Query= CharProtDB::CH_122457 (599 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_199 Length = 349 Score = 183 bits (465), Expect = 9e-51 Identities = 124/311 (39%), Positives = 171/311 (54%), Gaps = 17/311 (5%) Query: 7 TVRIVEVGPRDGLQNIPQSIDSTIKLDLIRRLRDAGLQTIELTSFVSPRAIPQLADAQVV 66 TVR EVG RDGLQ+I + + K++ + AG + IE+ SFV R +PQLAD V Sbjct: 42 TVR--EVGLRDGLQSIATVVSTAQKIEWLNAAYAAGQREIEVGSFVPARLLPQLADTADV 99 Query: 67 VQNADIQKLLKNPKLRLPVLVPNLKGLERALHNGIKEVAVFISATEGFSRANINCTVDEG 126 + +A K L P L VLVPN+KG ERAL G + V +SA+ S AN+ T DE Sbjct: 100 LAHA---KTL--PGLVASVLVPNVKGAERALECGADLMVVPLSASHAHSLANLRKTPDEV 154 Query: 127 LERARQVASRAASAGLS--VRGYVSCIFADPYDGPTRPSSVLRCTKALLDAGCYEVSLGD 184 + ++ + ++G S + G V F G S VLR +ALLDAG VSL D Sbjct: 155 VAEVARIRALRDASGRSTLIEGGVGTAFGCTLQGEVAESEVLRLMQALLDAGADHVSLAD 214 Query: 185 TLGIGTPADVRWLITYLQDNGVPLEMLAGHFHDTYGGAVANVWEAYKCGLRMFDSSVAGL 244 T+G PA V L + V + HFHDT G +ANV+ A++ G+ FD+ +AG+ Sbjct: 215 TVGFADPASVARLFDKARAL-VGDRLACAHFHDTRGMGLANVYAAWQTGITRFDACLAGI 273 Query: 245 GGCPXALGAKGNVASEDLVYMFERSGIHTGVDLSKLVETGEWISRQLSIAISSRAGAALW 304 GGCP A GA GNV +EDLV+M ER G+ TG+D+S L+ + ++ L AG L Sbjct: 274 GGCPHAPGASGNVTTEDLVFMLERMGVATGIDVSALLALRQRVAGWL-------AGETLH 326 Query: 305 AMRKQTAVPKS 315 Q +P++ Sbjct: 327 GTLWQAGLPQN 337 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: 430 Number of extensions: 21 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 599 Length of database: 349 Length adjustment: 33 Effective length of query: 566 Effective length of database: 316 Effective search space: 178856 Effective search space used: 178856 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