Align arylformamidase (EC 3.5.1.9) (characterized)
to candidate AZOBR_RS18020 AZOBR_RS18020 esterase
Query= metacyc::MONOMER-19505 (304 letters) >FitnessBrowser__azobra:AZOBR_RS18020 Length = 284 Score = 140 bits (353), Expect = 3e-38 Identities = 95/275 (34%), Positives = 128/275 (46%), Gaps = 4/275 (1%) Query: 18 QYSPSTTVPSLQAYLDDYRRISADARRRHPVRAGLAYGPHPAELLDYFPATGRSDAPLLV 77 QY+P +VP + + +S AR R+ R +AYG P LD FPA APL V Sbjct: 11 QYNPRHSVPDFARHAERAAALSRAARERNAGRYDIAYGDTPLSTLDVFPAAAPG-APLHV 69 Query: 78 FVHGGNWQALGRAESAFAVPALLAAGAAVAVVEYGLAPDTPLEAMAGMVRRSVAWLLRHA 137 F+HGG W+ +A+ ++ AL+ G V+ Y L P L +A R + W+ R+A Sbjct: 70 FLHGGYWRGRDKADYSYVADALVPRGVTTVVMNYDLCPAATLPEIARRTREGLRWIHRNA 129 Query: 138 DALGFAPDRLHLCGTSAGAHLAAMALLPHPDDGPD--TSGRIAGAVLLSGIYDLEPVQLS 195 +LG PDRL + G SAGAHL AMAL G D G I AVL+SGIY+L PV Sbjct: 130 ASLGGDPDRLTVSGHSAGAHLIAMALAEDAGAGADRLEDGAIKAAVLISGIYELAPVLDI 189 Query: 196 YVNDALRLDGAGARRNSPLLRLPPRLPPLVVARGDNETEEYVRQHEQMVAALRARAA-VT 254 VN+ + L SP+ P L V G ET ++ Q + R + T Sbjct: 190 TVNETIGLRPEMVDGVSPMRHPPSTATALTVVVGSAETPAWIAQSRDFATLCQCRGSRCT 249 Query: 255 EVVAERRDHFDLPYDLGVRGTGLGDAVLAQLGLAE 289 DHF + + L VL G+ E Sbjct: 250 YHTLAGEDHFSIMARMERPDDTLSRLVLDAAGVKE 284 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: 230 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: 284 Length adjustment: 26 Effective length of query: 278 Effective length of database: 258 Effective search space: 71724 Effective search space used: 71724 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