Align arylformamidase (EC 3.5.1.9) (characterized)
to candidate HSERO_RS05590 HSERO_RS05590 esterase
Query= metacyc::MONOMER-19505 (304 letters) >FitnessBrowser__HerbieS:HSERO_RS05590 Length = 277 Score = 147 bits (371), Expect = 3e-40 Identities = 95/260 (36%), Positives = 131/260 (50%), Gaps = 12/260 (4%) Query: 6 VYRGMDRATLDRQYSPSTTVPSLQAYLDDYRRISADARRRHPVRAGLAYGPHPAELLDYF 65 +YR LD QY+ VP Q Y D + R AR+ HP A L YG + +D+F Sbjct: 3 IYRDYTSEELDAQYNVRARVPDFQDYFDRFARQGEAARQAHPHLADLPYGEETLQSIDFF 62 Query: 66 PATGRSDAPLLVFVHGGNWQALGRAESAFAVPALLAAGAAVAVVEYGLAPDTPLEAMAGM 125 PA PLLVF+HGG W++L + + + L VA++ Y LAP + +A Sbjct: 63 PAHSNG-RPLLVFIHGGYWRSLDKHQFSHLALPYLEQDINVALINYRLAPQVRMGDIAAD 121 Query: 126 VRRSVAWLLRHADALGFAPDRLHLCGTSAGAHLAAM--ALLPHPDDGPDTSGRIAGAVLL 183 R++ L A AL + + L G SAGAHLA + AL P + G L Sbjct: 122 CGRALRLLHAKAPALRVDANAIWLMGHSAGAHLACVIAALRAAP---------VRGVCAL 172 Query: 184 SGIYDLEPVQLSYVNDALRLDGAGARRNSPLLRLPPRLPPLVVARGDNETEEYVRQHEQM 243 SG+YDLEP++LSY+N+AL L A ++ SPLL P V+ G E+EE++RQ + Sbjct: 173 SGLYDLEPIRLSYLNEALHLSPADVQQASPLLLAMPDGVRAVLCAGGQESEEFLRQRDVY 232 Query: 244 VAALRARAAVTEVVAERRDH 263 A LR EVV + H Sbjct: 233 AANLRQSGHQVEVVEAAQAH 252 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: 10 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: 277 Length adjustment: 26 Effective length of query: 278 Effective length of database: 251 Effective search space: 69778 Effective search space used: 69778 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