Align arylformamidase (EC 3.5.1.9) (characterized)
to candidate SMa0259 SMa0259 hypothetical protein
Query= metacyc::MONOMER-19505 (304 letters) >FitnessBrowser__Smeli:SMa0259 Length = 281 Score = 126 bits (317), Expect = 5e-34 Identities = 90/264 (34%), Positives = 125/264 (47%), Gaps = 7/264 (2%) Query: 25 VPSLQAYLDDYRRISADARRRHPVRAGLAYGPHPAELLDYF-PATGRSDAPLLVFVHGGN 83 VP ++ S R VRA + YG E++D P ++ APL VFVHGG Sbjct: 13 VPDFDTIAAEFAERSWAVSARADVRADIRYGSGVREVIDLILPERVQAGAPLHVFVHGGY 72 Query: 84 WQALGRAESAFAVPALLAAGAAVAVVEYGLAPDTPLEAMAGMVRRSVAWLLRHADALGFA 143 W++ + F +LAAG A+VEY L P L+ + VRRSV WL HA G Sbjct: 73 WRSGEKINYRFVAAPVLAAGGIAALVEYDLMPGKRLDVLVDQVRRSVLWLQAHAGDFGAD 132 Query: 144 PDRLHLCGTSAGAHLAAMALLPHPDDG-PDTSGRIAGAVLLSGIYDLEPVQLSYVNDALR 202 P RL + G SAGAHLA+ P++ P + + G +LLSGIYDL + S++ Sbjct: 133 PARLTVSGHSAGAHLASFLAATGPEEAYPPSLPTLQGLLLLSGIYDLSGIPDSFLRHEAE 192 Query: 203 LDGAGARRNSPLLRLPPRLPPLVVARGDNETEEYVRQHEQMVAALRARAAVTEVV-AERR 261 + A SPL P ++A G +ET + Q + LRA+ E++ Sbjct: 193 MTPMEAAAWSPLTSSQLPCPLRIIAYGADETAPFQNQAAGLCELLRAQDKSAELLPVPDL 252 Query: 262 DHFDLPYDL----GVRGTGLGDAV 281 +H + DL GV G L D V Sbjct: 253 NHMSIVLDLADTDGVLGRQLHDLV 276 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: 183 Number of extensions: 11 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: 281 Length adjustment: 26 Effective length of query: 278 Effective length of database: 255 Effective search space: 70890 Effective search space used: 70890 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