Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate WP_011383741.1 AMB_RS06760 fumarate hydratase
Query= BRENDA::P0AC33 (548 letters) >NCBI__GCF_000009985.1:WP_011383741.1 Length = 538 Score = 732 bits (1890), Expect = 0.0 Identities = 355/532 (66%), Positives = 425/532 (79%) Query: 6 FHYQAPFPLKKDDTEYYLLTSEHVSVSEFEGQEILKVAPEALTLLARQAFHDASFMLRPA 65 F + FPL DDT Y +T+E V + F GQ ++ VAPEA+T L ++A D S +LRPA Sbjct: 4 FAFHELFPLSHDDTPYRKITAEGVGTASFNGQSVVTVAPEAITALTKEAIKDTSHLLRPA 63 Query: 66 HQQQVADILRDPEASENDKYVALQFLRNSDIAAKGVLPTCQDTGTAIIVGKKGQRVWTGG 125 H QQ+ +IL D +S ND++VA L+N+ IA+ GVLP CQDTGTAI++GKKGQRVWTGG Sbjct: 64 HLQQLRNILDDAGSSPNDRFVAYDLLKNACIASGGVLPMCQDTGTAIVMGKKGQRVWTGG 123 Query: 126 GDEAALARGVYNTYIEDNLRYSQNAPLDMYKEVNTGTNLPAQIDLYAVDGDEYKFLCIAK 185 DEAA+++GV Y E NLRYSQ APLDMY+EVNTGTNLPAQIDLYA +G+ YKF+ +AK Sbjct: 124 NDEAAISKGVQEAYTELNLRYSQTAPLDMYEEVNTGTNLPAQIDLYATEGEAYKFMFMAK 183 Query: 186 GGGSANKTYLYQETKALLTPGKLKNYLVEKMRTLGTAACPPYHIAFVIGGTSAETNLKTV 245 GGGSANKT+LYQ+TKALL P L ++L ++RTLGT+ACPPYH+A VIGG SAE LKTV Sbjct: 184 GGGSANKTFLYQQTKALLNPKSLLSFLDAQIRTLGTSACPPYHLAIVIGGLSAEMCLKTV 243 Query: 246 KLASAKYYDELPTEGNEHGQAFRDVELEKELLIEAQNLGLGAQFGGKYFAHDIRVIRLPR 305 KLASAKY D LPT GN+ GQAFRD+ELE+ +L Q++G+GAQFGGKYF HD+RVIRLPR Sbjct: 244 KLASAKYLDSLPTAGNKFGQAFRDLELEQIVLKMTQDMGIGAQFGGKYFCHDVRVIRLPR 303 Query: 306 HGASCPVGMGVSCSADRNIKAKINRQGIWIEKLEHNPGKYIPEELRKAGEGEAVRVDLNR 365 HGASCPV +GVSCSADR I KI + G+++E +E +P KY+P+ GE V++DLNR Sbjct: 304 HGASCPVAIGVSCSADRQILGKITKDGVYVEAMEKDPAKYLPDVDPSKLAGEVVKIDLNR 363 Query: 366 PMKEILAQLSQYPVSTRLSLNGTIIVGRDIAHAKLKERMDNGEGLPQYIKDHPIYYAGPA 425 PM EI LSQYPV TR+SL G +IV RDIAHAKLKER+D GEGLP+Y K +YYAGPA Sbjct: 364 PMDEIRKTLSQYPVKTRVSLTGPMIVARDIAHAKLKERLDRGEGLPEYFKQMGVYYAGPA 423 Query: 426 KTPEGYASGSLGPTTAGRMDSYVDQLQAQGGSMIMLAKGNRSQQVTDACKKHGGFYLGSI 485 KTP +ASGS GPTTAGRMDSYVDQ QA GGSM+M+AKGNRS+ VT+ACKKHGGFYLGSI Sbjct: 424 KTPSNFASGSFGPTTAGRMDSYVDQFQAAGGSMLMIAKGNRSKAVTEACKKHGGFYLGSI 483 Query: 486 GGPAAVLAQGSIKSLECVEYPELGMEAIWKIEVEDFPAFILVDDKGNDFFQQ 537 GG AA LAQ IK +E +EYPELGMEAIW+IEV DFPAFI+VDDKGNDFF + Sbjct: 484 GGAAARLAQDCIKKVEVIEYPELGMEAIWRIEVVDFPAFIVVDDKGNDFFAE 535 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: 957 Number of extensions: 42 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: 538 Length adjustment: 35 Effective length of query: 513 Effective length of database: 503 Effective search space: 258039 Effective search space used: 258039 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