Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate H281DRAFT_04956 H281DRAFT_04956 fumarase, class I, homodimeric
Query= BRENDA::Q141Z6 (520 letters) >FitnessBrowser__Burk376:H281DRAFT_04956 Length = 507 Score = 985 bits (2546), Expect = 0.0 Identities = 492/507 (97%), Positives = 500/507 (98%) Query: 14 MTVIKQEDLIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCAE 73 MTVIKQEDLIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCAE Sbjct: 1 MTVIKQEDLIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCAE 60 Query: 74 GKRPICQDTGIVTVFVKVGMDVRWDGATMGVTDMINEGVRRGYLNPDNVLRASIVSPPEG 133 GKRPICQDTGIVTVFVKVGMDVRWDGATMGVTDMINEGVRRGYLNPDNVLRASIVSPPEG Sbjct: 61 GKRPICQDTGIVTVFVKVGMDVRWDGATMGVTDMINEGVRRGYLNPDNVLRASIVSPPEG 120 Query: 134 GRKNTKDNTPAVIHYEIVPGNTVDVQVAAKGGGSENKSKFAMLNPSDSIVDWILKTVPTM 193 RKNTKDNTPAVIHYEIVPG+ VDVQVAAKGGGSENKSKFAMLNPSDSIVDWILKTVPTM Sbjct: 121 ARKNTKDNTPAVIHYEIVPGDKVDVQVAAKGGGSENKSKFAMLNPSDSIVDWILKTVPTM 180 Query: 194 GAGWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPKDWIEELRVELHEKVNA 253 GAGWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPKDWIEELRVELHEKVNA Sbjct: 181 GAGWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPKDWIEELRVELHEKVNA 240 Query: 254 LGIGAQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHAHFTLDGSGAARLEAPSL 313 LGIGAQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHAHFTLDGSG A+LEAPSL Sbjct: 241 LGIGAQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHAHFTLDGSGVAKLEAPSL 300 Query: 314 DAWPKVHWQPDTEKSKRVDLNTLTPEEVAAWTPGQTLLLSGKMLTGRDAAHKRIADMLAK 373 DAWPKV W+P+TE SKRVDLNTLTPEEVA+W PGQTLLLSGKMLTGRDAAHKRIADMLAK Sbjct: 301 DAWPKVQWEPNTETSKRVDLNTLTPEEVASWKPGQTLLLSGKMLTGRDAAHKRIADMLAK 360 Query: 374 GEKLPVDFTNRVIYYVGPVDPVRDEAVGPAGPTTATRMDKFTEMMLAQTGLISMIGKAER 433 GEKLPVDFTNRVIYYVGPVDPVRDEAVGPAGPTTATRMDKFTE ML+QTGLISMIGKAER Sbjct: 361 GEKLPVDFTNRVIYYVGPVDPVRDEAVGPAGPTTATRMDKFTETMLSQTGLISMIGKAER 420 Query: 434 GPVAIEAIRKHKAAYLMAVGGAAYLVSKAIRSAKVLAFEDLGMEAIYEFDVQDMPVTVAV 493 GPVAIEAIRKHKAAYLMAVGGAAYLVSKAIRSAKVLAFEDLGMEAIYEFDVQDMPVTVAV Sbjct: 421 GPVAIEAIRKHKAAYLMAVGGAAYLVSKAIRSAKVLAFEDLGMEAIYEFDVQDMPVTVAV 480 Query: 494 DSNGTSVHQTGPKEWQARIGKIPVATV 520 DS+GTSVHQTGPKEWQA+IGKIPVATV Sbjct: 481 DSSGTSVHQTGPKEWQAKIGKIPVATV 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: 1068 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