Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_009546068.1 CCE_RS03960 1,4-dihydroxy-2-naphthoyl-CoA synthase
Query= BRENDA::Q1D5Y4 (258 letters) >NCBI__GCF_000017845.1:WP_009546068.1 Length = 277 Score = 102 bits (255), Expect = 6e-27 Identities = 81/256 (31%), Positives = 124/256 (48%), Gaps = 25/256 (9%) Query: 16 TIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDK-----AFCAGAD--LKE 68 TI+ +RNA + EL + + +++TGAG AFC+G D ++ Sbjct: 26 TINRPHKRNAFRPKTVFELYDAFCDAREDSSIGVILLTGAGPHTDGKYAFCSGGDQSVRG 85 Query: 69 RATMAEDE--VRAFLDGLRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAPAA 126 +A +D R + L+R R++ K V IA + G A+GGG L + CDL +AA A Sbjct: 86 QAGYVDDAGIPRLNVLDLQRLIRSMPK---VVIALVAGYAIGGGHVLHVICDLTIAADNA 142 Query: 127 ELGLTEVKLGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPEGHL 186 G T K+G GG G LAR++G +A+++ R+ NA +A +GL N + P L Sbjct: 143 VFGQTGPKVGSFDGGFGASYLARIIGQKKAREIWFLCRQYNAEQALEMGLVNCVVPVEQL 202 Query: 187 LAVAYGLAESVVENAPIAVATAKHAI----DEGTGLELDDALALELRKYEEIL--KTEDR 240 A+ ++ +PIA+ K A D GL+ EL +L TE+ Sbjct: 203 ETEGVQWAKEILSKSPIAIRCLKAAFNADCDGQAGLQ-------ELAGNATLLYYMTEEG 255 Query: 241 LEGLRAFAEKRAPVYK 256 EG +AF EKR P ++ Sbjct: 256 AEGKQAFLEKRPPNFR 271 Lambda K H 0.319 0.136 0.380 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: 148 Number of extensions: 7 Number of successful extensions: 3 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: 258 Length of database: 277 Length adjustment: 25 Effective length of query: 233 Effective length of database: 252 Effective search space: 58716 Effective search space used: 58716 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: 47 (22.7 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