Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate RR42_RS13905 RR42_RS13905 fumarate hydratase
Query= BRENDA::Q141Z6 (520 letters) >FitnessBrowser__Cup4G11:RR42_RS13905 Length = 507 Score = 942 bits (2434), Expect = 0.0 Identities = 461/507 (90%), Positives = 487/507 (96%) Query: 14 MTVIKQEDLIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCAE 73 MTVIKQEDLIQS+ADSLQYISYYHP+DYI +LGRAYELEQSPAAKDAIAQILTNSRMCAE Sbjct: 1 MTVIKQEDLIQSVADSLQYISYYHPMDYITSLGRAYELEQSPAAKDAIAQILTNSRMCAE 60 Query: 74 GKRPICQDTGIVTVFVKVGMDVRWDGATMGVTDMINEGVRRGYLNPDNVLRASIVSPPEG 133 GKRPICQDTGIVT+FVKVGMDVRWD ATMG++DMINEGVRRGY NPDNVLRASIVSPPEG Sbjct: 61 GKRPICQDTGIVTIFVKVGMDVRWDDATMGLSDMINEGVRRGYTNPDNVLRASIVSPPEG 120 Query: 134 GRKNTKDNTPAVIHYEIVPGNTVDVQVAAKGGGSENKSKFAMLNPSDSIVDWILKTVPTM 193 GRKNTKDNTPAVIHYE+VPGNTVD+QVAAKGGGSENKSKF MLNPSDSIVDW+LKTVPTM Sbjct: 121 GRKNTKDNTPAVIHYEVVPGNTVDIQVAAKGGGSENKSKFVMLNPSDSIVDWVLKTVPTM 180 Query: 194 GAGWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPKDWIEELRVELHEKVNA 253 GAGWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGP+DWIEE+RVEL+EKVNA Sbjct: 181 GAGWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPQDWIEEMRVELYEKVNA 240 Query: 254 LGIGAQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHAHFTLDGSGAARLEAPSL 313 LGIGAQGLGGLATVLDVKIM PTHAASKPVA+IPNCAATRH HFTLDGSG A+LEAP L Sbjct: 241 LGIGAQGLGGLATVLDVKIMGYPTHAASKPVAMIPNCAATRHVHFTLDGSGPAKLEAPDL 300 Query: 314 DAWPKVHWQPDTEKSKRVDLNTLTPEEVAAWTPGQTLLLSGKMLTGRDAAHKRIADMLAK 373 AWPKV W P+TE SKRVDLNTLTP EVA+W PGQTLLL+GKMLTGRDAAHKRIADMLAK Sbjct: 301 SAWPKVEWAPNTETSKRVDLNTLTPAEVASWKPGQTLLLNGKMLTGRDAAHKRIADMLAK 360 Query: 374 GEKLPVDFTNRVIYYVGPVDPVRDEAVGPAGPTTATRMDKFTEMMLAQTGLISMIGKAER 433 GEKLPVDFTNRVIYYVGPVDPVRDEAVGPAGPTTATRMDKFTEMMLA+TGLISMIGKAER Sbjct: 361 GEKLPVDFTNRVIYYVGPVDPVRDEAVGPAGPTTATRMDKFTEMMLAETGLISMIGKAER 420 Query: 434 GPVAIEAIRKHKAAYLMAVGGAAYLVSKAIRSAKVLAFEDLGMEAIYEFDVQDMPVTVAV 493 GPVAIEAI+KHK+AYLMAVGGAAYLV+KAIR AKV+ FEDLGMEAIYEFDV+DMPVTVAV Sbjct: 421 GPVAIEAIKKHKSAYLMAVGGAAYLVAKAIRHAKVVGFEDLGMEAIYEFDVKDMPVTVAV 480 Query: 494 DSNGTSVHQTGPKEWQARIGKIPVATV 520 DS GTSVH+TGP EWQA+IGKIPVA + Sbjct: 481 DSEGTSVHKTGPAEWQAKIGKIPVAAL 507 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: 1069 Number of extensions: 28 Number of successful extensions: 1 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: 507 Length adjustment: 35 Effective length of query: 485 Effective length of database: 472 Effective search space: 228920 Effective search space used: 228920 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