Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate GFF1166 HP15_1143 hydro-lyase, Fe-S type, tartrate/fumarate subfamily, alpha subunit
Query= BRENDA::Q141Z6 (520 letters) >FitnessBrowser__Marino:GFF1166 Length = 504 Score = 728 bits (1878), Expect = 0.0 Identities = 355/498 (71%), Positives = 423/498 (84%), Gaps = 2/498 (0%) Query: 15 TVIKQEDLIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCAEG 74 TVI+Q+DLI+S+AD+LQ+ISYYHP D+I + AY+ E+S AAKDA+AQIL NSRMCAEG Sbjct: 3 TVIRQDDLIESVADALQFISYYHPKDFIDGVYEAYQKEESQAAKDAMAQILINSRMCAEG 62 Query: 75 KRPICQDTGIVTVFVKVGMDVRWDGATMGVTDMINEGVRRGYLNPDNVLRASIVSPPEGG 134 RP+CQDTGIVTVFV +GM+V+WD + + D+INEGVRR Y +PDNVLRASI+ P+G Sbjct: 63 HRPLCQDTGIVTVFVNIGMNVQWD-CELPLDDVINEGVRRAYTHPDNVLRASILDDPDGK 121 Query: 135 RKNTKDNTPAVIHYEIVPGNTVDVQVAAKGGGSENKSKFAMLNPSDSIVDWILKTVPTMG 194 RKNT DNTPA+IHY++VPG+TV+V VAAKGGGSE KSKFAMLNPSDS+VDW+LK VP MG Sbjct: 122 RKNTGDNTPAIIHYKMVPGDTVEVHVAAKGGGSEAKSKFAMLNPSDSVVDWVLKMVPQMG 181 Query: 195 AGWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPKDWIEELRVELHEKVNAL 254 AGWCPPGMLGIGIGGTAEKAM MAKESL+DPIDI D+ ARG + EELR+EL +KVN L Sbjct: 182 AGWCPPGMLGIGIGGTAEKAMEMAKESLLDPIDIHDLKARGASNRAEELRLELFDKVNDL 241 Query: 255 GIGAQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHAHFTLDGSGAARLEAPSLD 314 GIGAQGLGGL TVLDVK+ PTHAA+KPVAIIPNCAATRHAHFTLDG+G + P L+ Sbjct: 242 GIGAQGLGGLTTVLDVKVKDYPTHAANKPVAIIPNCAATRHAHFTLDGTGPSLQTPPRLE 301 Query: 315 AWPKVHWQPDTEKSKRVDLNTLTPEEVAAWTPGQTLLLSGKMLTGRDAAHKRIADMLAKG 374 WP++ W+ + +RV+L+T+TPE+V W PG+T+LLSGKMLTGRDAAHK++ DM+ KG Sbjct: 302 DWPEITWEVG-DNVRRVNLDTVTPEDVKDWQPGETVLLSGKMLTGRDAAHKKMVDMIEKG 360 Query: 375 EKLPVDFTNRVIYYVGPVDPVRDEAVGPAGPTTATRMDKFTEMMLAQTGLISMIGKAERG 434 E+LPVD R IYYVGPVDPVR+E VGPAGPTTATRMDKFT ML +TGL MIGKAERG Sbjct: 361 EELPVDLKGRFIYYVGPVDPVREEVVGPAGPTTATRMDKFTHTMLEKTGLTGMIGKAERG 420 Query: 435 PVAIEAIRKHKAAYLMAVGGAAYLVSKAIRSAKVLAFEDLGMEAIYEFDVQDMPVTVAVD 494 VAI+AI++ A YLMAVGG+AYLVSKAI++A+V+AF +LGMEAIYEF+V+DMPVTVAVD Sbjct: 421 QVAIDAIKEFGAVYLMAVGGSAYLVSKAIKNAEVVAFPELGMEAIYEFEVEDMPVTVAVD 480 Query: 495 SNGTSVHQTGPKEWQARI 512 S G+SVHQTGP EW +I Sbjct: 481 SRGSSVHQTGPAEWHEKI 498 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: 902 Number of extensions: 17 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