Align arylformamidase (EC 3.5.1.9) (characterized)
to candidate Ac3H11_1663 putative esterase
Query= metacyc::MONOMER-19505 (304 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1663 Length = 293 Score = 136 bits (343), Expect = 5e-37 Identities = 90/242 (37%), Positives = 129/242 (53%), Gaps = 14/242 (5%) Query: 11 DRATLDRQYSPSTTVPSLQAYLDDYRRISADARRRHPVRAGLAYGPHPAELLDYFPATGR 70 D A L+R Y+ VP YL + R SA R + P +AYG P E LD FP+T Sbjct: 7 DPAWLERMYNNRALVPDHMDYLQRWARDSAQVRAQVPCVLDVAYGTGPGETLDVFPSTRP 66 Query: 71 SDAPL--LVFVHGGNWQALGRAESAFAVPALLAAGAAVAVVEYGLAPDTP-----LEAMA 123 + AP+ LVF+HGG W+AL +++ +F P AG V VV Y L P TP + + Sbjct: 67 AGAPVPVLVFIHGGYWRALDKSDHSFIAPPFNQAGFCVVVVNYALCPGTPEAPVTIPHIV 126 Query: 124 GMVRRSVAWLLRHADALGFAPDRLHLCGTSAGAHLAAMALL---PHPDDG-PDTSGRIAG 179 + ++VAW+ R+ +A G R+ + G SAG HLAAM L P G PD G + Sbjct: 127 RQMEKAVAWVARNIEAHGGDARRITVAGHSAGGHLAAMLLTSVWPLIGAGLPD--GLVRN 184 Query: 180 AVLLSGIYDLEP-VQLSYVNDALRLDGAGARRNSPLLRLPPRLPPLVVARGDNETEEYVR 238 A+ +SG++DLEP + ++ +AL L ++SP L P L G +E+EE+ R Sbjct: 185 ALSISGLHDLEPLMHTPFLQEALHLTDQHVLQDSPARLLAPEHGILYCVAGGDESEEFHR 244 Query: 239 QH 240 Q+ Sbjct: 245 QN 246 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: 209 Number of extensions: 13 Number of successful extensions: 4 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: 293 Length adjustment: 27 Effective length of query: 277 Effective length of database: 266 Effective search space: 73682 Effective search space used: 73682 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