Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate GFF2242 PGA1_c22740 fatty acid oxidation complex subunit alpha
Query= BRENDA::Q13825 (339 letters) >FitnessBrowser__Phaeo:GFF2242 Length = 706 Score = 114 bits (285), Expect = 8e-30 Identities = 91/286 (31%), Positives = 138/286 (48%), Gaps = 40/286 (13%) Query: 77 LRVRHLEEENRGIVVLGINRAYGKNSLSKNLIKMLSKAVDALKSDKKVRTIIIRSEVPGI 136 + ++H E G+ + +N A N+L + ++LS A+ L +D++V+ I++ S +P + Sbjct: 2 ISIKHTE----GVAFIELN-APSVNALGLKMRQVLSSAIHELDADEQVKAIVLCSALP-L 55 Query: 137 FCAGADLKERAKMSSSEVGPFVSKIRAVINDIANLPVPTIAAIDGLALGGGLELALACDI 196 FC GAD+ E + + P + + +I P IAAI G A+GG LE+ALACD Sbjct: 56 FCGGADIVE-FRTGAVWDKPDLPDLCVMIETSKK---PIIAAIAGPAMGGALEIALACDY 111 Query: 197 RVAASSAKMGLVETKLAIIPGGGGTQRLPRAIGMSLAKELIFSARVLDGKEAKAVGLISH 256 RVA A MGL E KL ++PG GGTQRLPR G+ A ++I S + G+ A + GL+ Sbjct: 112 RVATPDAVMGLPEIKLGLLPGAGGTQRLPRIAGLEAATQMILSGDPVKGEYALSCGLVDA 171 Query: 257 VLEQNQ---------------EGDAAYRKALDLAREFLPQG---------------PVAM 286 + E +Q EGD A R P+G VA Sbjct: 172 LFENDQDFRAHVLGFATRVSHEGDPKRSCADMTVRHPDPKGYLTGFRDQIAHTSKNLVAP 231 Query: 287 RVAKLAINQGMEVDLVTGLAIEEACYAQTIPTKDRLEGLLAFKEKR 332 ++I E+ L GL E+A +A+ + T G F +R Sbjct: 232 ERCLVSIEAACEMPLAEGLEQEKAGFAELLDTPQSRAGRHLFFAER 277 Lambda K H 0.318 0.135 0.386 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: 462 Number of extensions: 21 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: 339 Length of database: 706 Length adjustment: 34 Effective length of query: 305 Effective length of database: 672 Effective search space: 204960 Effective search space used: 204960 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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