Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate 201373 SO2222 fumarate hydratase, class I, anaerobic, putative (NCBI ptt file)
Query= BRENDA::Q141Z6 (520 letters) >FitnessBrowser__MR1:201373 Length = 516 Score = 702 bits (1813), Expect = 0.0 Identities = 342/499 (68%), Positives = 409/499 (81%), Gaps = 3/499 (0%) Query: 16 VIKQEDLIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCAEGK 75 VIKQ D I+S+AD+LQYISYYHP D++ A+ AYE EQS AAKDAIAQIL NSRM AEGK Sbjct: 12 VIKQADFIESVADALQYISYYHPKDFVDAMSEAYEREQSAAAKDAIAQILINSRMSAEGK 71 Query: 76 RPICQDTGIVTVFVKVGMDVRWDGATMGVTDMINEGVRRGYLNPDNVLRASIVSPPEGGR 135 RP+CQDTGIVT FVKVGM V+WD M + M++EGVRR Y NPDN LRASIV+ P G R Sbjct: 72 RPLCQDTGIVTTFVKVGMGVKWDKTDMTIQQMVDEGVRRAYTNPDNPLRASIVADPAGSR 131 Query: 136 KNTKDNTPAVIHYEIVPGNTVDVQVAAKGGGSENKSKFAMLNPSDSIVDWILKTVPTMGA 195 KNTKDNTP+V+H ++VPGN V+V +AAKGGGSENK+K MLNPSD I W+ KT+PTMGA Sbjct: 132 KNTKDNTPSVVHIDMVPGNHVEVAIAAKGGGSENKAKMVMLNPSDDIAAWVEKTLPTMGA 191 Query: 196 GWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPKDWIEELRVELHEKVNALG 255 GWCPPGMLGIGIGGTAEKA V+AKE+LM+ +DI +++ARG + E+LR+++ E+ N LG Sbjct: 192 GWCPPGMLGIGIGGTAEKAAVLAKEALMESVDIHELMARGAQTTEEKLRLDIFERANNLG 251 Query: 256 IGAQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHAHFTLDGSGAARLEAPSLDA 315 IGAQGLGGL TVLDVKI +APTHAASKPV +IPNCAATRH HF LDG+G A L PSL Sbjct: 252 IGAQGLGGLTTVLDVKIKSAPTHAASKPVVMIPNCAATRHVHFHLDGTGPADLAPPSLSD 311 Query: 316 WPKVHWQPDTEKSKRVDLNTLTPEEVAAWTPGQTLLLSGKMLTGRDAAHKRIADMLAKGE 375 WP++ + ++ +RV+L+T+T ++ W G+TLLLSGKMLTGRDAAHKRI ++ GE Sbjct: 312 WPEITREVGSD-VRRVNLDTVTQADIEQWQSGETLLLSGKMLTGRDAAHKRIQSLIESGE 370 Query: 376 KLP--VDFTNRVIYYVGPVDPVRDEAVGPAGPTTATRMDKFTEMMLAQTGLISMIGKAER 433 LP VDFT + IYYVGPVDPV +E VGPAGPTTATRMDKFT++ML +TGL+ MIGKAER Sbjct: 371 GLPEGVDFTGKFIYYVGPVDPVGNEVVGPAGPTTATRMDKFTDLMLDKTGLMGMIGKAER 430 Query: 434 GPVAIEAIRKHKAAYLMAVGGAAYLVSKAIRSAKVLAFEDLGMEAIYEFDVQDMPVTVAV 493 GP +E+I+KHKA YLMAVGGAAYLVSKAI+ ++V+AF DLGMEAIYEFDVQDMPVTVAV Sbjct: 431 GPATVESIKKHKAVYLMAVGGAAYLVSKAIKKSRVVAFADLGMEAIYEFDVQDMPVTVAV 490 Query: 494 DSNGTSVHQTGPKEWQARI 512 DSNG + H+TGP W+ I Sbjct: 491 DSNGVNAHETGPAIWKVNI 509 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: 870 Number of extensions: 24 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: 516 Length adjustment: 35 Effective length of query: 485 Effective length of database: 481 Effective search space: 233285 Effective search space used: 233285 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