Align fumarylacetoacetate (FAA) hydrolase (EC 3.7.1.2) (characterized)
to candidate RR42_RS16615 RR42_RS16615 hypothetical protein
Query= reanno::psRCH2:GFF3447 (327 letters) >FitnessBrowser__Cup4G11:RR42_RS16615 Length = 331 Score = 247 bits (630), Expect = 3e-70 Identities = 140/322 (43%), Positives = 181/322 (56%), Gaps = 2/322 (0%) Query: 1 MKLATL-NQGRDGVLVVVSRDLAQAVKVPQIAATLQAALDDWNYCKPKLEAVYQRLNDGL 59 MKL T+ N RDG L + QA+ V I T+Q A+D W+ L Y+RL +G Sbjct: 1 MKLGTIDNWTRDGALALADTRSGQAIVVSHIVGTMQEAIDSWSKYSAPLHEEYRRLQEGT 60 Query: 60 EEGAFAFDQTACHSPLPRAYHWADGSAYVNHVELVRKARGAEMPESFWHDPLMYQGGADA 119 + +PLPRAY DG Y H+EL R PE P YQ +D+ Sbjct: 61 LCATVPISELRWRAPLPRAYQLLDGGGYRPHLELGFSMRKQSFPEEMAEKPSFYQSVSDS 120 Query: 120 FIPPHSPIRLADEAWGIDLEGELAVITDDVPMGATPAEAASHIQLLMLVNDVSLRNLIPG 179 + P L + G D E EL V+T+DV AT E A+ I L+ L+ND+SLR Sbjct: 121 ILGPTEDFILGTDDLGTDFEAELVVVTNDVKQMATKVEGANGILLVGLMNDISLRLTQRV 180 Query: 180 ELAKGFGFYQSKPSSSFSPVAVTPDELGETWRDGKVHRPLVSHINGELFGQPDAGTDMTF 239 E A+GFGFY KP + +P VTPDELGE W + KV P+ NGE+FG PD M F Sbjct: 181 EHARGFGFYHCKPKKTLAPFLVTPDELGEHWINFKVSLPVEVRWNGEVFGCPDGAEHMMF 240 Query: 240 NFPTLVAHAARTRPLGAGTIIGSGTVSNYDRSA-GSSCLAEKRMLEVVEHGEAKTPFLKF 298 +F TLV+ A+R R L AGTIIG GTV+ YDR G C+ E+R L+++E GE +T +LK Sbjct: 241 DFATLVSEASRHRKLTAGTIIGGGTVATYDRDTFGQCCILERRALDILEFGEERTSWLKP 300 Query: 299 GDRVRIEMFDAAGQSIFGAIDQ 320 DRVRIE+ G ++FGAIDQ Sbjct: 301 DDRVRIEVRMPDGSTVFGAIDQ 322 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: 359 Number of extensions: 20 Number of successful extensions: 2 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: 331 Length adjustment: 28 Effective length of query: 299 Effective length of database: 303 Effective search space: 90597 Effective search space used: 90597 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: 49 (23.5 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