Align fumarylacetoacetate (FAA) hydrolase (EC 3.7.1.2) (characterized)
to candidate WP_011906669.1 SARO_RS17985 2-keto-4-pentenoate hydratase
Query= reanno::psRCH2:GFF3447 (327 letters) >NCBI__GCF_000013325.1:WP_011906669.1 Length = 314 Score = 265 bits (678), Expect = 8e-76 Identities = 155/326 (47%), Positives = 201/326 (61%), Gaps = 19/326 (5%) Query: 1 MKLATLNQG-RDGVLVVVSRDLAQAVKVPQIAATLQAALDDWNYCKPKLEAVYQRLNDGL 59 M+LATL G +DG LVVVS D P TLQ AL+DW +P L A+ Sbjct: 1 MRLATLRDGTKDGRLVVVSPDGTACAPAP--VTTLQQALEDWVEVEPALRAI-------- 50 Query: 60 EEGAF--AFDQTACHSPLPRAYHWADGSAYVNHVELVRKARGAEMPESFWHDPLMYQGGA 117 AF D +PLPRA+ W DGSA+ +H +L+ G P + PLMYQG + Sbjct: 51 --AAFPDVLDPAQVMAPLPRAWQWLDGSAFQSHGDLMDAVLGITKPRT--DVPLMYQGTS 106 Query: 118 DAFIPPHSPIRLADEAWGIDLEGELAVITDDVPMGATPAEAASHIQLLMLVNDVSLRNLI 177 D F P ++ DEA GID EGE VI D VPMG + A+A HI+L++ +ND SLR L Sbjct: 107 DRFYGPTDDVKFPDEALGIDFEGEFGVIVDAVPMGTSAADAMGHIRLVVQINDWSLRTLA 166 Query: 178 PGELAKGFGFYQSKPSSSFSPVAVTPDELGETWRDGKVHRPLVSHINGELFGQPDAGTDM 237 E+ GFG+ Q+KP +P AVTP+ELG++W +G+V L NG FG + G M Sbjct: 167 GPEMKTGFGWVQAKPPCGMAPFAVTPEELGDSWHNGRVCLDLEVDWNGRRFGAAN-GEPM 225 Query: 238 TFNFPTLVAHAARTRPLGAGTIIGSGTVSNYD-RSAGSSCLAEKRMLEVVEHGEAKTPFL 296 F LVAHAARTR L AGT+IGSGTVSN + R GSSC+AE+R +EV++ GE KT F+ Sbjct: 226 GHGFHELVAHAARTRDLVAGTVIGSGTVSNANFREIGSSCIAERRGIEVIDLGEPKTEFM 285 Query: 297 KFGDRVRIEMFDAAGQSIFGAIDQQV 322 +FGD VR+E DA+G++ FGAI+Q+V Sbjct: 286 RFGDTVRMEAVDASGRAPFGAIEQKV 311 Lambda K H 0.318 0.135 0.411 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: 335 Number of extensions: 11 Number of successful extensions: 5 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: 327 Length of database: 314 Length adjustment: 28 Effective length of query: 299 Effective length of database: 286 Effective search space: 85514 Effective search space used: 85514 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 24 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