Align 2-oxopent-4-enoate hydratase (EC 4.2.1.80) (characterized)
to candidate BPHYT_RS07255 BPHYT_RS07255 4-oxalocrotonate decarboxylase
Query= metacyc::MONOMER-14738 (279 letters) >FitnessBrowser__BFirm:BPHYT_RS07255 Length = 257 Score = 136 bits (342), Expect = 5e-37 Identities = 77/236 (32%), Positives = 132/236 (55%), Gaps = 6/236 (2%) Query: 39 QPVAPLTDREADITIEDAYQIQLRMIQRRLDAGERVVGKKIGVTSKVVMDMLKVNQPDFG 98 +P+A +T A +++DAY IQ I+RR+ GE +VG K+G TS+ M + V+ +G Sbjct: 19 EPIAQIT-AAAPFSLDDAYVIQRASIERRIHRGESMVGVKLGFTSRAKMIQMGVDSLIWG 77 Query: 99 HLLSGMVYNEGQPIPVSSMIAPKAEAEVAFILARDLEGPGVTAADVLRATDCVMPCFEIV 158 L M+ +G I + I P+ E EV F+ +R+++ P +T + R + V P EI+ Sbjct: 78 WLTDAMLDEDGGRIALDRFIHPRVEPEVCFLTSREIDRP-LTLLEASRYLEAVAPAMEII 136 Query: 159 DSRIKDWKIKIQDTVADNASCGVLTLGGLRKSPRDLD-LALAGMVLEKNGEIISTSCGAS 217 DSR +D++ ++D VADN S L +G R D L AG+ + +G ++ A+ Sbjct: 137 DSRYRDFRFTLEDVVADNCSSAGLVIG---PWTRKFDGLRNAGVTMRIDGRLVQAGSTAA 193 Query: 218 VQGSPVNAVAWLANTLGRLGIGLKAGDIILSGSQSPLVPVVAGDSLYCSVGGLGGT 273 + G P+ ++ + L + G+ L AG +I++G+ + P+ A ++C+V GLG T Sbjct: 194 ILGDPLRSIVQASRLLTQSGLALPAGSLIMAGAATAAHPLTANAHVHCAVNGLGST 249 Lambda K H 0.318 0.136 0.390 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: 135 Number of extensions: 5 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: 279 Length of database: 257 Length adjustment: 25 Effective length of query: 254 Effective length of database: 232 Effective search space: 58928 Effective search space used: 58928 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