Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate BWI76_RS16275 BWI76_RS16275 fumarate hydratase FumA
Query= BRENDA::P0AC33 (548 letters) >FitnessBrowser__Koxy:BWI76_RS16275 Length = 548 Score = 1001 bits (2588), Expect = 0.0 Identities = 488/548 (89%), Positives = 520/548 (94%) Query: 1 MSNKPFHYQAPFPLKKDDTEYYLLTSEHVSVSEFEGQEILKVAPEALTLLARQAFHDASF 60 MSNKPF YQ PFPLKKDDTEYYLL+S++VSV+EF GQE+LKV P+ALTLLA+ AFHDASF Sbjct: 1 MSNKPFVYQDPFPLKKDDTEYYLLSSDYVSVAEFAGQEVLKVEPQALTLLAQHAFHDASF 60 Query: 61 MLRPAHQQQVADILRDPEASENDKYVALQFLRNSDIAAKGVLPTCQDTGTAIIVGKKGQR 120 MLRPAHQQQVADIL DPEASENDKYVALQFLRNSDIAAKGVLPTCQDTGTAII GKKGQR Sbjct: 61 MLRPAHQQQVADILNDPEASENDKYVALQFLRNSDIAAKGVLPTCQDTGTAIITGKKGQR 120 Query: 121 VWTGGGDEAALARGVYNTYIEDNLRYSQNAPLDMYKEVNTGTNLPAQIDLYAVDGDEYKF 180 VWTGGGDEAALA+GVYNTYI+DNLRYSQNAPLDMYKEVNTGTNLPAQIDLYA DG+EYKF Sbjct: 121 VWTGGGDEAALAQGVYNTYIQDNLRYSQNAPLDMYKEVNTGTNLPAQIDLYATDGEEYKF 180 Query: 181 LCIAKGGGSANKTYLYQETKALLTPGKLKNYLVEKMRTLGTAACPPYHIAFVIGGTSAET 240 LCIAKGGGSANKTYLYQETKAL+TP KLKNYLVEKMRTLGTAACPPYHIAFVIGGTSAE+ Sbjct: 181 LCIAKGGGSANKTYLYQETKALITPAKLKNYLVEKMRTLGTAACPPYHIAFVIGGTSAES 240 Query: 241 NLKTVKLASAKYYDELPTEGNEHGQAFRDVELEKELLIEAQNLGLGAQFGGKYFAHDIRV 300 LKTVKLAS KYYD LPTEGNEHGQAFRD++LE+ELL EAQNLGLGAQFGGKYFAHDIRV Sbjct: 241 TLKTVKLASTKYYDGLPTEGNEHGQAFRDIQLEQELLAEAQNLGLGAQFGGKYFAHDIRV 300 Query: 301 IRLPRHGASCPVGMGVSCSADRNIKAKINRQGIWIEKLEHNPGKYIPEELRKAGEGEAVR 360 IRLPRHGASCPVGMGVSCSADRNIKAKINR+GIW+EKLE NPGKYIPE LR+AGEGEAV+ Sbjct: 301 IRLPRHGASCPVGMGVSCSADRNIKAKINREGIWLEKLESNPGKYIPEHLRQAGEGEAVK 360 Query: 361 VDLNRPMKEILAQLSQYPVSTRLSLNGTIIVGRDIAHAKLKERMDNGEGLPQYIKDHPIY 420 V+LN+PM +ILA LSQYPVSTRLSL+GTIIV RDIAHAKLKE +D+GE LPQY+KDHPIY Sbjct: 361 VNLNQPMSDILALLSQYPVSTRLSLSGTIIVARDIAHAKLKELIDSGEELPQYVKDHPIY 420 Query: 421 YAGPAKTPEGYASGSLGPTTAGRMDSYVDQLQAQGGSMIMLAKGNRSQQVTDACKKHGGF 480 YAGPAKTP+GYASGSLGPTTAGRMDSYVD LQ+ G SM+MLAKGNRSQQVTDAC KHGGF Sbjct: 421 YAGPAKTPDGYASGSLGPTTAGRMDSYVDLLQSHGASMVMLAKGNRSQQVTDACHKHGGF 480 Query: 481 YLGSIGGPAAVLAQGSIKSLECVEYPELGMEAIWKIEVEDFPAFILVDDKGNDFFQQIQL 540 YLGSIGGPAAVLAQ SI+SLECV YPELGMEAIWKIEVE+FPAFILVDDKGNDFFQQIQ Sbjct: 481 YLGSIGGPAAVLAQQSIRSLECVAYPELGMEAIWKIEVENFPAFILVDDKGNDFFQQIQS 540 Query: 541 TQCTRCVK 548 +QC RCVK Sbjct: 541 SQCARCVK 548 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: 1171 Number of extensions: 32 Number of successful extensions: 1 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: 548 Length adjustment: 36 Effective length of query: 512 Effective length of database: 512 Effective search space: 262144 Effective search space used: 262144 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 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