Align Methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate AZOBR_RS22290 AZOBR_RS22290 enoyl-CoA hydratase
Query= reanno::pseudo6_N2E2:Pf6N2E2_2193 (272 letters) >FitnessBrowser__azobra:AZOBR_RS22290 Length = 264 Score = 238 bits (608), Expect = 8e-68 Identities = 127/249 (51%), Positives = 170/249 (68%) Query: 15 GVATLWLSRESKNNAFNAEMIRELILALDHVSSDPNLRFLLIRGRGKHFSAGADLAWMQQ 74 GVAT+ ++R +NAFN +I +L A+ + S+P++R +L+RG GK FSAGADL WM++ Sbjct: 16 GVATVTMNRAEVHNAFNERVIADLTDAVLSLGSNPDVRAILLRGAGKSFSAGADLGWMKK 75 Query: 75 SAELDYHTNLDDARELAELMYNLAKLKIPTLAVVQGAAFGGALGLISACDMAIGADEAQF 134 A + N++DA LA ++ L + PT+AVVQG AFGG +GL++ACD+AI A+ A F Sbjct: 76 MAGYSHGENVEDAMGLATMLRTLDECPKPTIAVVQGPAFGGGVGLVAACDIAIAAEAASF 135 Query: 135 CLSEVRIGLAPAVISPFVVQAIGERAARRYALTAERFDGQRAKEIGLLSESYPAEVLDQQ 194 L+EVR+GL PAVISP+VV A+GERA RRY LTAERF A +GLL ++ PA LD Sbjct: 136 ALTEVRLGLIPAVISPYVVAAMGERACRRYFLTAERFSAAEALRLGLLHQTVPAAELDAA 195 Query: 195 VEQWIDNLLLNSPAAMRASKELLREVGNGALTPALRRYTENAIARIRVSPEGQEGLRAFL 254 VE + NLL PA+ A+KEL+R V L AL R T IAR R S EG+EG+ AFL Sbjct: 196 VEVMVRNLLQCGPASQTAAKELIRAVARRPLNDALVRDTAERIARQRASDEGREGVGAFL 255 Query: 255 QKRAPNWQA 263 +KR P W++ Sbjct: 256 EKREPAWRS 264 Lambda K H 0.318 0.133 0.382 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: 208 Number of extensions: 5 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: 272 Length of database: 264 Length adjustment: 25 Effective length of query: 247 Effective length of database: 239 Effective search space: 59033 Effective search space used: 59033 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: 47 (22.7 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