Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate RR42_RS02195 RR42_RS02195 fumarate hydratase
Query= BRENDA::Q141Z6 (520 letters) >FitnessBrowser__Cup4G11:RR42_RS02195 Length = 291 Score = 116 bits (291), Expect = 9e-31 Identities = 85/275 (30%), Positives = 129/275 (46%), Gaps = 22/275 (8%) Query: 38 PLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCAEGKRPICQDTGIVTVFVKVGMDVRW 97 P D + + E E S A+ +A + N R+ E +CQDTG+ + +G + Sbjct: 24 PPDVKDGIAQLQENETSATARSVLATMSKNIRIAQETDNLLCQDTGVPIYNMTIGTGIAV 83 Query: 98 DGATMGVTDMINEGVRRGY--LNPDNVLRASIVSPPEGGRKNTKDNTPA-VIH--YEIVP 152 DG + +RRG ++ LR+S+V P +T VIH ++ P Sbjct: 84 DGRAF------KQAIRRGCERATREHPLRSSVVHPLTRKNNHTSCGIEVPVIHIDFDDTP 137 Query: 153 GNTVDVQVAAKGGGSENKSKFAMLNPS---DSIVDWILKTVPTMGAGWCPPGMLGIGIGG 209 G + + + KG GSEN S M P+ D+I +++ +V G CPP ++G+G+GG Sbjct: 138 GR-MTLAMVPKGSGSENNSFLKMAIPAEGMDAIKTFVIDSVIAAGGKTCPPTIVGVGLGG 196 Query: 210 TAEKAMVMAKESLMDPIDIQDVIARGPKDWIEELRVELHEKVNALGIGAQGLGGLATVLD 269 T++ + +AK + + + G L EL VN LG+G QGLGG AT Sbjct: 197 TSDLCVALAKRAATRALGTRCADPDGAA-----LEAELSRAVNQLGVGPQGLGGDATAFA 251 Query: 270 VKIMAAPTHAASKPVAIIPNCAATRH--AHFTLDG 302 V I A TH P+A+ C + R A FT DG Sbjct: 252 VHIELASTHITMNPIAVNMQCHSARRACATFTADG 286 Lambda K H 0.316 0.133 0.392 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: 347 Number of extensions: 15 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: 520 Length of database: 291 Length adjustment: 30 Effective length of query: 490 Effective length of database: 261 Effective search space: 127890 Effective search space used: 127890 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: 41 (21.6 bits) S2: 50 (23.9 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