Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate WP_069957537.1 BEN30_RS06515 fumarate hydratase
Query= BRENDA::P0AC33 (548 letters) >NCBI__GCF_001746755.1:WP_069957537.1 Length = 549 Score = 749 bits (1935), Expect = 0.0 Identities = 363/537 (67%), Positives = 435/537 (81%), Gaps = 1/537 (0%) Query: 3 NKPFHYQAPFPLKKDDTEYYLLTSEHVSVSEFEGQEILKVAPEALTLLARQAFHDASFML 62 N+P ++ F D+TEY LLT E VS G+ IL++ PE L+LLA A D S +L Sbjct: 2 NEPAFHEL-FSFGPDETEYRLLTKEFVSTHTVSGRTILEIEPEGLSLLASTAMRDTSHLL 60 Query: 63 RPAHQQQVADILRDPEASENDKYVALQFLRNSDIAAKGVLPTCQDTGTAIIVGKKGQRVW 122 RPAH +Q+A IL+DPEAS ND++VA++ L+N++I+A GVLP CQDTGTAII+GKKG+ VW Sbjct: 61 RPAHLKQLASILKDPEASANDRFVAMELLKNANISAGGVLPMCQDTGTAIIMGKKGENVW 120 Query: 123 TGGGDEAALARGVYNTYIEDNLRYSQNAPLDMYKEVNTGTNLPAQIDLYAVDGDEYKFLC 182 TGG DEAAL+ GV Y E+NLRYSQ APL M+KEV TGTNLPAQID+ AV G YKF+ Sbjct: 121 TGGQDEAALSEGVMKAYAENNLRYSQMAPLSMFKEVGTGTNLPAQIDIGAVPGGSYKFMF 180 Query: 183 IAKGGGSANKTYLYQETKALLTPGKLKNYLVEKMRTLGTAACPPYHIAFVIGGTSAETNL 242 +AKGGGSANKT+L+Q+T ALL P + +L ++ TLGTAACPPYH+A VIGG SAE NL Sbjct: 181 MAKGGGSANKTFLHQKTAALLNPKSMAEFLKAEIATLGTAACPPYHLAVVIGGLSAELNL 240 Query: 243 KTVKLASAKYYDELPTEGNEHGQAFRDVELEKELLIEAQNLGLGAQFGGKYFAHDIRVIR 302 KTVK+ASA Y D LPT+GN +GQAFRD+E+E E+L QNLG+GAQFGGKYF HD+RVIR Sbjct: 241 KTVKMASAHYLDGLPTQGNAYGQAFRDLEMEAEILKMTQNLGIGAQFGGKYFCHDVRVIR 300 Query: 303 LPRHGASCPVGMGVSCSADRNIKAKINRQGIWIEKLEHNPGKYIPEELRKAGEGEAVRVD 362 LPRHGASCPVG+GVSCSADR I KI +GI++EKLE +P KY+PE K + V +D Sbjct: 301 LPRHGASCPVGIGVSCSADRQILGKITAEGIFLEKLETDPAKYLPEITEKNLSDDVVSID 360 Query: 363 LNRPMKEILAQLSQYPVSTRLSLNGTIIVGRDIAHAKLKERMDNGEGLPQYIKDHPIYYA 422 LN+PM +I AQLSQYP+ TR+ L G++IVGRD+AHAKLKER+D G+GLP YIK+HP+YYA Sbjct: 361 LNQPMDQIRAQLSQYPIKTRIKLTGSLIVGRDLAHAKLKERLDAGQGLPDYIKNHPVYYA 420 Query: 423 GPAKTPEGYASGSLGPTTAGRMDSYVDQLQAQGGSMIMLAKGNRSQQVTDACKKHGGFYL 482 GPAKTPEGYASGS GPTTAGRMDSYVDQ Q GGS++MLAKGNRSQ VTDACKKHGGFYL Sbjct: 421 GPAKTPEGYASGSFGPTTAGRMDSYVDQFQEAGGSLVMLAKGNRSQAVTDACKKHGGFYL 480 Query: 483 GSIGGPAAVLAQGSIKSLECVEYPELGMEAIWKIEVEDFPAFILVDDKGNDFFQQIQ 539 GSIGG AA LA SIK +EC+EYPELGMEAIWKI++ DFPAFI+VDDKGNDFF+ I+ Sbjct: 481 GSIGGAAAELAFESIKHIECIEYPELGMEAIWKIDIVDFPAFIIVDDKGNDFFEDIK 537 Lambda K H 0.317 0.135 0.397 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: 986 Number of extensions: 45 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: 548 Length of database: 549 Length adjustment: 36 Effective length of query: 512 Effective length of database: 513 Effective search space: 262656 Effective search space used: 262656 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: 53 (25.0 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