Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate N515DRAFT_4003 N515DRAFT_4003 fumarase, class I, homodimeric
Query= BRENDA::Q141Z6 (520 letters) >FitnessBrowser__Dyella79:N515DRAFT_4003 Length = 504 Score = 791 bits (2042), Expect = 0.0 Identities = 390/504 (77%), Positives = 449/504 (89%), Gaps = 3/504 (0%) Query: 14 MTVIKQEDLIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCAE 73 MT IKQ+DLIQS+AD+LQYISYYHP+DYI L +AYE E+SPAA+DA+AQIL NSRM AE Sbjct: 1 MTTIKQDDLIQSVADALQYISYYHPVDYITNLAQAYEREESPAARDAMAQILINSRMAAE 60 Query: 74 GKRPICQDTGIVTVFVKVGMDVRWDGATMGVTDMINEGVRRGYLNPDNVLRASIVSPPEG 133 G RP+CQDTGIVTVF+KVGM+VRWD AT+ + DM+NEGVRR Y +PDN LRAS+++ P G Sbjct: 61 GHRPLCQDTGIVTVFLKVGMNVRWD-ATLSLEDMVNEGVRRAYNHPDNKLRASVLADPAG 119 Query: 134 GRKNTKDNTPAVIHYEIVPGNTVDVQVAAKGGGSENKSKFAMLNPSDSIVDWILKTVPTM 193 R NT+DNTPAVI+ IVPG+TV+V VAAKGGGSE KSKFAMLNPSDSIVDW+LKTVPTM Sbjct: 120 KRLNTRDNTPAVINVSIVPGDTVEVIVAAKGGGSEAKSKFAMLNPSDSIVDWVLKTVPTM 179 Query: 194 GAGWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPKDWIEELRVELHEKVNA 253 GAGWCPPGMLGIGIGGTAEKAM++AKESLM+ IDIQ++IARGP++ IEELR+EL+EKVNA Sbjct: 180 GAGWCPPGMLGIGIGGTAEKAMLLAKESLMEHIDIQELIARGPQNRIEELRLELYEKVNA 239 Query: 254 LGIGAQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHAHFTLDGSGAARLEAPSL 313 LGIGAQGLGGL TVLDVKI PTHAA+ PVA+IPNCAATRHAHFTLDGSG LEAPSL Sbjct: 240 LGIGAQGLGGLTTVLDVKIKDYPTHAANLPVAMIPNCAATRHAHFTLDGSGPVMLEAPSL 299 Query: 314 DAWPKVHWQPDTEKSKRVDLNTLTPEEVAAWTPGQTLLLSGKMLTGRDAAHKRIADMLAK 373 + WPK+ + D+ K +RVDL+T+T E+VA+W PG+ LLL+GK+LTGRDAAHKR+ DML K Sbjct: 300 EHWPKLTY--DSSKGRRVDLDTITREDVASWKPGEVLLLNGKLLTGRDAAHKRMVDMLNK 357 Query: 374 GEKLPVDFTNRVIYYVGPVDPVRDEAVGPAGPTTATRMDKFTEMMLAQTGLISMIGKAER 433 GE LPVDF R IYYVGPVDPVRDE VGPAGPTTATRMDKFTE +LAQTGL+ M+GKAER Sbjct: 358 GEPLPVDFKGRFIYYVGPVDPVRDEVVGPAGPTTATRMDKFTEQVLAQTGLLGMVGKAER 417 Query: 434 GPVAIEAIRKHKAAYLMAVGGAAYLVSKAIRSAKVLAFEDLGMEAIYEFDVQDMPVTVAV 493 GP AIEAI++H++ YLMAVGGAAYLVSKAI+S++V+ F DLGMEAIYEFDV+DMPVTVAV Sbjct: 418 GPAAIEAIKQHQSVYLMAVGGAAYLVSKAIKSSRVVGFADLGMEAIYEFDVKDMPVTVAV 477 Query: 494 DSNGTSVHQTGPKEWQARIGKIPV 517 DS GTSVHQTGPKEWQARIGKIPV Sbjct: 478 DSAGTSVHQTGPKEWQARIGKIPV 501 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: 896 Number of extensions: 27 Number of successful extensions: 3 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: 504 Length adjustment: 35 Effective length of query: 485 Effective length of database: 469 Effective search space: 227465 Effective search space used: 227465 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