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) >lcl|FitnessBrowser__Koxy:BWI76_RS16275 BWI76_RS16275 fumarate hydratase FumA 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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