Align Methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate 7024492 Shewana3_1670 methylglutaconyl-CoA hydratase (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_01590 (273 letters) >FitnessBrowser__ANA3:7024492 Length = 286 Score = 227 bits (579), Expect = 2e-64 Identities = 122/252 (48%), Positives = 165/252 (65%), Gaps = 2/252 (0%) Query: 15 GVATLWLSRESKNNAFNAEMIRELILALDHVSSDPNLRFLLIRGRGKHFSAGADLAWMQQ 74 GV L L+R +NAF+ MI E+I L + + + + L+++ GK+FSAGADL WM++ Sbjct: 32 GVGELILNRAEVHNAFDEVMISEMIAVLGYFAEHKDCKLLVLKANGKNFSAGADLNWMRK 91 Query: 75 SAELDYHTNLDDARELAELMYNLAKLKIPTLAVVQGAAFGGALGLISACDMAIGADEAQF 134 A++D+ NL+DA+ LA+LM +L PT+A+VQGAAFGGALGLI A D+AI + A F Sbjct: 92 QAKMDFEQNLNDAKALAKLMQDLDTFPKPTIALVQGAAFGGALGLICASDIAIATERASF 151 Query: 135 CLSEVRIGLAPAVISPFVVQAIGERAARRYALTAERFDGQRAKEIGLLSESYPVETLDQQ 194 CLSEV++GL PAVISP+V +A+G RA+RRY LTAERFD Q A ++ ++ E + L Sbjct: 152 CLSEVKLGLIPAVISPYVARAMGNRASRRYMLTAERFDAQTALKLNVIHEIN--DDLAAA 209 Query: 195 VEQWIDNLLLNSPAAMRASKELLREVGNGALTPALRRYTENAIARIRVSPEGQEGLRAFL 254 + I L NSP M K LL + +G + YT IARIRVS EGQEGL AF Sbjct: 210 AQPIITALQANSPQGMAWVKTLLARLEDGVIDQDTIDYTSERIARIRVSDEGQEGLNAFF 269 Query: 255 QKRAPNWQAESN 266 +KR PNW ++ Sbjct: 270 EKRQPNWHTPTD 281 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: 216 Number of extensions: 3 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: 273 Length of database: 286 Length adjustment: 26 Effective length of query: 247 Effective length of database: 260 Effective search space: 64220 Effective search space used: 64220 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