Align arylformamidase (EC 3.5.1.9) (characterized)
to candidate Ga0059261_3763 Ga0059261_3763 Esterase/lipase
Query= metacyc::MONOMER-19505 (304 letters) >FitnessBrowser__Korea:Ga0059261_3763 Length = 286 Score = 100 bits (250), Expect = 3e-26 Identities = 92/254 (36%), Positives = 118/254 (46%), Gaps = 31/254 (12%) Query: 52 LAYGPHPAELLDYFPATGRSDA-PLLVFVHGGNWQALGR--AESAFAVPALLAAGAAVAV 108 +A+G P + LD++PA S A PL VFVHGG W+ + A A + G A A Sbjct: 33 IAFGADPLQRLDFYPAANASGAAPLFVFVHGGGWKRGDKRNATGAAKIAHFTGRGHAFAS 92 Query: 109 VEYGLAPDTPLEAMAGMVRRSVAWLLRHADALGFAPDRLHLCGTSAGAHLAAMA-----L 163 V Y L PD +E A V ++A L+R A +LG P R+ L G SAGAHL+A+ Sbjct: 93 VNYRLVPDARVEDQAQDVANAIARLIRDARSLGVDPGRIVLAGHSAGAHLSALVATDPQY 152 Query: 164 LPHPDDGPDTSGRIAGAVLLSG-IYDLEPVQLS--------YVNDALRLDGAGARRNSPL 214 L G + RI G +LL G YD+ PVQ A D A R SP Sbjct: 153 LRRAGVGME---RIKGVILLDGAAYDV-PVQAGEGPGIMRPTYTQAFGTDPARQRALSPT 208 Query: 215 LR-LPPRLPPLVVARGDNETEEYVRQHEQMVAALRARAAVTEVVAER----RDHFDLPYD 269 L P P ++ E E+ RQ E + AALR EV A R R H ++ Sbjct: 209 LHAAAPNAPRFLILH--VEREDGRRQSEALAAALRKAGTQAEVRALRGRGLRGHMEINRA 266 Query: 270 LG---VRGTGLGDA 280 LG GTG+ DA Sbjct: 267 LGDPDYPGTGIVDA 280 Lambda K H 0.319 0.136 0.402 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: 219 Number of extensions: 12 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: 304 Length of database: 286 Length adjustment: 26 Effective length of query: 278 Effective length of database: 260 Effective search space: 72280 Effective search space used: 72280 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: 48 (23.1 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