Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_008342913.1 BA79_RS08330 1,4-dihydroxy-2-naphthoyl-CoA synthase
Query= BRENDA::A4YI89 (259 letters) >NCBI__GCF_000691145.1:WP_008342913.1 Length = 272 Score = 127 bits (318), Expect = 3e-34 Identities = 87/256 (33%), Positives = 129/256 (50%), Gaps = 31/256 (12%) Query: 17 ITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFCAGAD--------- 66 IT+NRP NA K + EL A S+A + ++ VI++ G G KAFC+G D Sbjct: 25 ITINRPHVHNAFTPKTVSELIDAFSRARDNSDVGVIVLAGAGGKAFCSGGDQKVRGHGGY 84 Query: 67 -----ITQFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIR 121 I + N L ++ I + KP IAM+ GYA+GGG L + CD+ Sbjct: 85 VGDDQIPRLNVL-------------DLQRLIRVIPKPVIAMVAGYAIGGGHVLHVVCDLT 131 Query: 122 IAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRV 181 IAA+ A G +G + G+ L R++G +A E+ + ++A GLVN V Sbjct: 132 IAADNAIFGQTGPKVGSFDAGYGSGYLARIVGHKKAREIWYLCRQYNAQEALDMGLVNTV 191 Query: 182 VPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGL-ALESVGWGVVFSTED 240 VPL LE+ET K E + +KSP +L +K N D L+G+ + ++T++ Sbjct: 192 VPLEQLEEETVKWCEDMLEKSPTALRFLKAAFNADTDG--LAGIQQFAGDATLLYYTTDE 249 Query: 241 KKEGVSAFLEKREPTF 256 KEG +F EKR+P F Sbjct: 250 AKEGRDSFKEKRKPDF 265 Lambda K H 0.315 0.135 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: 149 Number of extensions: 9 Number of successful extensions: 4 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: 259 Length of database: 272 Length adjustment: 25 Effective length of query: 234 Effective length of database: 247 Effective search space: 57798 Effective search space used: 57798 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: 42 (22.0 bits) S2: 47 (22.7 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