Align Methylglutaconyl-CoA hydratase, mitochondrial; AU-specific RNA-binding enoyl-CoA hydratase; AU-binding enoyl-CoA hydratase; muAUH; Itaconyl-CoA hydratase; EC 4.2.1.18; EC 4.2.1.56 (characterized)
to candidate WP_090441622.1 BLS63_RS06660 crotonase
Query= SwissProt::Q9JLZ3 (314 letters) >NCBI__GCF_900100495.1:WP_090441622.1 Length = 267 Score = 112 bits (281), Expect = 7e-30 Identities = 81/250 (32%), Positives = 124/250 (49%), Gaps = 18/250 (7%) Query: 69 INRAYGKNALSKNLLKMLSKAVDALKSDKKVRTIIIRSEVPGIFCAGADLK---ERAKMH 125 +NRA N +S L + +AL + +VR I++R+ V F +G D+K E + H Sbjct: 32 LNRA-PLNVISMGQRDQLRQVFEALDAHPQVRVIVLRA-VGEHFSSGGDIKGFLEASPEH 89 Query: 126 SSEVGPFVSKIRSVINDIANLPVPTIAAIDGLALGGGLELALACDIRVAASSAKMGLVET 185 VSK+ + P IAA G G G EL+LACD R+A+ + + L E Sbjct: 90 -------VSKLAWNVAAPVRCEKPVIAANRGYTFGVGFELSLACDFRIASETTRYALPEQ 142 Query: 186 KLAIIPGGGGTQRLPRAIGMSLAKELIFSARVLDGQEAKAVGLISHVLEQNQEGDAAYRK 245 L IPG GG+ RL + IG++ K ++ A+ + G++A G+ + + DA Sbjct: 143 NLGQIPGSGGSARLQKIIGVARTKHMVMRAKRISGEQAYEWGIATECV-----ADAELES 197 Query: 246 ALD-LAREFLPQGPVAMRVAKLAINQGMEVDLVTGLAIEEACYAQTISTKDRLEGLLAFK 304 +D L E P+A R AK IN + L + +E CY++ S+ D EG+ AF Sbjct: 198 TVDALVDELRRFSPLAQRTAKRLINDNEDAPLSVAIEMEGHCYSRLRSSYDFKEGVEAFH 257 Query: 305 EKRPPRYKGE 314 KRP ++GE Sbjct: 258 SKRPAVFRGE 267 Lambda K H 0.318 0.135 0.377 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: 146 Number of extensions: 4 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: 314 Length of database: 267 Length adjustment: 26 Effective length of query: 288 Effective length of database: 241 Effective search space: 69408 Effective search space used: 69408 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 24 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