Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate RR42_RS27740 RR42_RS27740 fumarate hydratase
Query= BRENDA::Q141Z6 (520 letters) >FitnessBrowser__Cup4G11:RR42_RS27740 Length = 497 Score = 608 bits (1568), Expect = e-178 Identities = 306/493 (62%), Positives = 372/493 (75%), Gaps = 4/493 (0%) Query: 14 MTVIKQEDLIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCAE 73 M VI QED++ SIAD+LQY+SYYHP+D++QAL RA+ E + AA+DAI Q+L NSRM AE Sbjct: 1 MIVIFQEDVVDSIADALQYVSYYHPVDFVQALKRAFAAEPAGAARDAIEQLLVNSRMSAE 60 Query: 74 GKRPICQDTGIVTVFVKVGMDVRW---DGATM-GVTDMINEGVRRGYLNPDNVLRASIVS 129 RPICQDTG+ VF+ VGMDVR+ DGA + V M++ VRRGY + N LRA++V Sbjct: 61 AHRPICQDTGVAQVFMTVGMDVRFAARDGAALLSVQQMVDAAVRRGYTHSANPLRATMVG 120 Query: 130 PPEGGRKNTKDNTPAVIHYEIVPGNTVDVQVAAKGGGSENKSKFAMLNPSDSIVDWILKT 189 G R+NT DNTP + E+VPGNT+ + V AKGGG + K+KFA LNPSDS+VDWIL Sbjct: 121 SALGERRNTGDNTPGFLQLELVPGNTIKMTVVAKGGGGDVKAKFATLNPSDSLVDWILAA 180 Query: 190 VPTMGAGWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPKDWIEELRVELHE 249 +P MGAGWCPPG+LG+G+GGT E+AM+ AK +L PIDI + +GP + E LR+ L E Sbjct: 181 IPQMGAGWCPPGVLGVGVGGTPEQAMLAAKRALFSPIDIHALRDKGPANDTERLRLALFE 240 Query: 250 KVNALGIGAQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHAHFTLDGSGAARLE 309 ++NALGIGAQGLGGLATVLDVK+ A P HAA+ PVA+IPNCAATR LDGSG ARLE Sbjct: 241 RINALGIGAQGLGGLATVLDVKVAALPCHAATLPVALIPNCAATRFVTVELDGSGPARLE 300 Query: 310 APSLDAWPKVHWQPDTEKSKRVDLNTLTPEEVAAWTPGQTLLLSGKMLTGRDAAHKRIAD 369 P D W + + + VDL+ L +VA W G+TL L G++LT RDAAHKR+ Sbjct: 301 PPPADTWDGIPGALTAKPGRVVDLDNLDAAQVAQWQVGETLRLRGRLLTARDAAHKRLVA 360 Query: 370 MLAKGEKLPVDFTNRVIYYVGPVDPVRDEAVGPAGPTTATRMDKFTEMMLAQTGLISMIG 429 ML GE LPV NR IYYVGPVD V DEAVGPAGPTTATRMDKF +L QTGL+ MIG Sbjct: 361 MLDAGEPLPVPLRNRAIYYVGPVDAVGDEAVGPAGPTTATRMDKFVPQLLEQTGLLLMIG 420 Query: 430 KAERGPVAIEAIRKHKAAYLMAVGGAAYLVSKAIRSAKVLAFEDLGMEAIYEFDVQDMPV 489 KAERGPVAIEAIR+H AAYL+AVGGAAYL+S+AIR A+VLAF +LGMEAIYEF+V+DMP Sbjct: 421 KAERGPVAIEAIRRHGAAYLIAVGGAAYLISRAIRKARVLAFAELGMEAIYEFEVEDMPA 480 Query: 490 TVAVDSNGTSVHQ 502 TVAVD+ G S+H+ Sbjct: 481 TVAVDATGRSIHR 493 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: 793 Number of extensions: 32 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: 520 Length of database: 497 Length adjustment: 34 Effective length of query: 486 Effective length of database: 463 Effective search space: 225018 Effective search space used: 225018 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: 52 (24.6 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