Align arylformamidase (EC 3.5.1.9) (characterized)
to candidate RR42_RS16840 RR42_RS16840 aylformamidase
Query= metacyc::MONOMER-19505 (304 letters) >FitnessBrowser__Cup4G11:RR42_RS16840 Length = 309 Score = 137 bits (346), Expect = 2e-37 Identities = 105/293 (35%), Positives = 144/293 (49%), Gaps = 15/293 (5%) Query: 11 DRATLDRQYSPSTTVPSLQAYLDDYRRISADARRRHPVRAGLAY-----GPHPA-ELLDY 64 D A R+Y+ VP ++ + +S R+R L+Y GPH A E LDY Sbjct: 17 DPAFYAREYNNRANVPDNATHMAHWAELSRQVRKRAGWLEDLSYAGAEPGPHAADERLDY 76 Query: 65 FPAT-GRSDAP--LLVFVHGGNWQALGRAESAFAVPALLAAGAAVAVVEYGLAPDTPLEA 121 FPA G +D P LLVFVHGG W+AL + + + AL G +VAV+ Y L P +E Sbjct: 77 FPAEPGATDGPPPLLVFVHGGYWRALDKRDHSLVANALPRCGVSVAVINYSLCPAVTVET 136 Query: 122 MAGMVRRSVAWLLRHADALGFAPDRLHLCGTSAGAHLAAMALLP-HPDDGPD-TSGRIAG 179 + RSVAWL R + LG R+ + G S G H+AAM L P G D + + G Sbjct: 137 IVLQAVRSVAWLYRESGRLGHDKARIFVGGHSVGGHMAAMMLTTLWPRVGRDLPADLVKG 196 Query: 180 AVLLSGIYDLEPV-QLSYVNDALRLDGAGARRNSPLLRLPPRLPPLVVARGDNETEEYVR 238 V +SG++DLEP+ + ++ L+L R SP P PLV A G E EY R Sbjct: 197 VVSVSGLHDLEPLRRADFLQVDLKLSARDVDRLSPAFLPPATDAPLVTAVGGLEPGEYHR 256 Query: 239 QHEQMVAALRARA---AVTEVVAERRDHFDLPYDLGVRGTGLGDAVLAQLGLA 288 Q + + AA A A V R HF++ +D + L AV +G+A Sbjct: 257 QTDLLRAAWLANAQAPGAAHVPMPDRHHFNVMHDFADGDSPLLLAVRRMMGVA 309 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: 223 Number of extensions: 9 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: 309 Length adjustment: 27 Effective length of query: 277 Effective length of database: 282 Effective search space: 78114 Effective search space used: 78114 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