Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate WP_057687166.1 ABB28_RS14895 fumarate hydratase
Query= BRENDA::Q141Z6 (520 letters) >NCBI__GCF_001431535.1:WP_057687166.1 Length = 505 Score = 779 bits (2012), Expect = 0.0 Identities = 381/504 (75%), Positives = 440/504 (87%), Gaps = 2/504 (0%) Query: 14 MTVIKQEDLIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCAE 73 MT IKQEDLIQSIAD+LQYISYYHP+DYI++L AYE E+SPAAK+A+AQIL NSRMCAE Sbjct: 1 MTSIKQEDLIQSIADALQYISYYHPVDYIKSLAAAYEREESPAAKEAMAQILINSRMCAE 60 Query: 74 GKRPICQDTGIVTVFVKVGMDVRWDGATMGVTDMINEGVRRGYLNPDNVLRASIVSPPEG 133 G RPICQDTGIVTVF+++GM+VRWD ATMGV DM NEGVRR Y +PDN LRAS+++ P G Sbjct: 61 GHRPICQDTGIVTVFLEIGMNVRWDDATMGVEDMANEGVRRAYNHPDNKLRASVLADPAG 120 Query: 134 GRKNTKDNTPAVIHYEIVPGNTVDVQVAAKGGGSENKSKFAMLNPSDSIVDWILKTVPTM 193 R NT+DNTP V++ ++VPG+TV+V VAAKGGGSE KSKFAMLNPSDSIVDW+LKTVPTM Sbjct: 121 KRINTRDNTPGVVNVKVVPGDTVEVIVAAKGGGSEAKSKFAMLNPSDSIVDWVLKTVPTM 180 Query: 194 GAGWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPKDWIEELRVELHEKVNA 253 GAGWCPPGMLGIGIGGTAEKAM++AKESLM+PIDI ++ ARG + EELR+EL +KVNA Sbjct: 181 GAGWCPPGMLGIGIGGTAEKAMLLAKESLMEPIDINELKARGASNRAEELRLELFDKVNA 240 Query: 254 LGIGAQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHAHFTLDGSGAARLEAPSL 313 LGIGAQGLGGL TVLD+K+ PTHAA+ PVA+IPNCAATRHAHFTLDGSG L+ PSL Sbjct: 241 LGIGAQGLGGLTTVLDIKVKDFPTHAANLPVAMIPNCAATRHAHFTLDGSGPVMLDPPSL 300 Query: 314 DAWPKVHWQPDTEKSKRVDLNTLTPEEVAAWTPGQTLLLSGKMLTGRDAAHKRIADMLAK 373 + WP++ + D K RVDL+T+TPE+VA+W PGQTLLL+GK+LTGRDAAHKRI +ML K Sbjct: 301 EDWPQITY--DASKGTRVDLDTITPEDVASWKPGQTLLLNGKLLTGRDAAHKRIVEMLDK 358 Query: 374 GEKLPVDFTNRVIYYVGPVDPVRDEAVGPAGPTTATRMDKFTEMMLAQTGLISMIGKAER 433 GE LPVD R IYYVGPVDPVRDE VGPAGPTTATRMDKFT +L QTGL+ M+GKAER Sbjct: 359 GEPLPVDLKGRFIYYVGPVDPVRDEVVGPAGPTTATRMDKFTRQVLEQTGLLGMVGKAER 418 Query: 434 GPVAIEAIRKHKAAYLMAVGGAAYLVSKAIRSAKVLAFEDLGMEAIYEFDVQDMPVTVAV 493 GP AIEAIR +++AYLMAVGG+AYLVSKAI++A+V+ F DLGMEAIYEF VQDMPVTVAV Sbjct: 419 GPAAIEAIRDNRSAYLMAVGGSAYLVSKAIKAARVVGFADLGMEAIYEFTVQDMPVTVAV 478 Query: 494 DSNGTSVHQTGPKEWQARIGKIPV 517 DS G SVHQTGP+EWQARIGKIPV Sbjct: 479 DSTGESVHQTGPREWQARIGKIPV 502 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: 915 Number of extensions: 26 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: 505 Length adjustment: 35 Effective length of query: 485 Effective length of database: 470 Effective search space: 227950 Effective search space used: 227950 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 24 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