Align FAA hydrolase family protein (characterized, see rationale)
to candidate BPHYT_RS07330 BPHYT_RS07330 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase
Query= uniprot:A0A2E7P912 (281 letters) >FitnessBrowser__BFirm:BPHYT_RS07330 Length = 306 Score = 176 bits (447), Expect = 4e-49 Identities = 96/202 (47%), Positives = 128/202 (63%), Gaps = 11/202 (5%) Query: 79 NYADHAAESNLPI-PAE---PVVFNKWTSAVVGPNDDVKIPRGSKKTDWEVELGVVIGKG 134 NY +HA E + P E P +F K ++VV +V IP +++ DWEVEL VVIGK Sbjct: 99 NYYEHAREMGTELAPREESTPYMFMKAETSVVPTLAEVVIPPHAERVDWEVELAVVIGKT 158 Query: 135 GSYIDEKDAMSHVAGYCVVNDVSEREYQIERG----GTWDKGKGCDTFGPIGPWLVTRDE 190 G +I ++DA ++AGY ++NDVS R+ W +GK DTFGP+GPW V R Sbjct: 159 GRHIAQQDAYDYIAGYTILNDVSARDLNRRTDYPFKHDWFRGKSFDTFGPLGPWFVPRAC 218 Query: 191 VADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVISTGTPPGVGMG 250 +A+PQ L M L V+G+ Q+GNTS MIF +A + YLS ++LQPGD+I+TGTP GVGMG Sbjct: 219 IAEPQNLRMRLSVNGEMMQDGNTSGMIFNIAEQIEYLSTILTLQPGDLIATGTPTGVGMG 278 Query: 251 VKPEAVYLRAGQTMRLGIDGLG 272 VYL+AG M IDG+G Sbjct: 279 ---RGVYLKAGDVMVASIDGIG 297 Lambda K H 0.316 0.138 0.419 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: 251 Number of extensions: 15 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: 281 Length of database: 306 Length adjustment: 26 Effective length of query: 255 Effective length of database: 280 Effective search space: 71400 Effective search space used: 71400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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