Align 2-oxopent-4-enoate hydratase (EC 4.2.1.80) (characterized)
to candidate RR42_RS31850 RR42_RS31850 2-keto-4-pentenoate hydratase
Query= metacyc::MONOMER-14738 (279 letters) >FitnessBrowser__Cup4G11:RR42_RS31850 Length = 260 Score = 294 bits (753), Expect = 1e-84 Identities = 150/254 (59%), Positives = 183/254 (72%) Query: 24 IQHYGDELYQSLLDRQPVAPLTDREADITIEDAYQIQLRMIQRRLDAGERVVGKKIGVTS 83 I G+EL+Q+L R PVAPL+ R IT+ DAY+IQ + + RL G+R+ GKKIGVTS Sbjct: 6 IASLGEELHQALTARVPVAPLSGRGDPITVRDAYRIQQQFVAHRLAHGDRITGKKIGVTS 65 Query: 84 KVVMDMLKVNQPDFGHLLSGMVYNEGQPIPVSSMIAPKAEAEVAFILARDLEGPGVTAAD 143 V ML V+QPDFG LL+ M Y +GQPIP +++I P+AE E+AF L RDL GPGVT AD Sbjct: 66 LPVQQMLDVHQPDFGMLLASMRYPDGQPIPAATLIQPRAEGEIAFFLKRDLRGPGVTRAD 125 Query: 144 VLRATDCVMPCFEIVDSRIKDWKIKIQDTVADNASCGVLTLGGLRKSPRDLDLALAGMVL 203 VL AT+ V CFEIVDSRI DW+I+I+DTVADNASCG LG R SP LDLA M L Sbjct: 126 VLAATEAVSACFEIVDSRILDWRIRIEDTVADNASCGAYVLGEERVSPAGLDLAGCAMTL 185 Query: 204 EKNGEIISTSCGASVQGSPVNAVAWLANTLGRLGIGLKAGDIILSGSQSPLVPVVAGDSL 263 EKNG +++T G++ G P AVAWLANTLG LGIGL AG+ ILSGS + L+PVVAGD L Sbjct: 186 EKNGVVVATGQGSAALGHPAEAVAWLANTLGALGIGLLAGETILSGSLAALIPVVAGDRL 245 Query: 264 YCSVGGLGGTSVRF 277 + + G+G S RF Sbjct: 246 HLRIDGIGSCSTRF 259 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: 240 Number of extensions: 12 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: 279 Length of database: 260 Length adjustment: 25 Effective length of query: 254 Effective length of database: 235 Effective search space: 59690 Effective search space used: 59690 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