Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate Dsui_0926 Dsui_0926 fumarate hydratase, class II
Query= BRENDA::Q9LCC6 (468 letters) >FitnessBrowser__PS:Dsui_0926 Length = 463 Score = 358 bits (918), Expect = e-103 Identities = 195/458 (42%), Positives = 274/458 (59%), Gaps = 1/458 (0%) Query: 6 RIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEVGL 65 R+E D G +P + +G QT R+ E+F I+ + PELI++L +VK++AA N E+GL Sbjct: 4 RLEHDTFGPIAVPAERLWGAQTQRSLEHFAISSETMPPELIRALALVKQAAAQVNGELGL 63 Query: 66 LDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEKGN 125 L V I AADEV+ G+ +F + Q G+GT NMN NEV+ANRA EL+G +G Sbjct: 64 LPPPVAGAIAAAADEVLAGRHPAEFPLSVWQTGSGTQSNMNMNEVLANRASELLGGPRGE 123 Query: 126 YSKISPNSHVNMSQSTNDAFPTATHIAV-LSLLNQLIETTKYMQQEFMKKADEFAGVIKM 184 + PN VN+ QS+ND FPTA H+A L++ +L+ ++Q KA+ FA +IK+ Sbjct: 124 GRLVHPNDQVNLGQSSNDIFPTAIHVAATLAVDGRLLPALAELRQALAAKAEAFADLIKI 183 Query: 185 GRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEYIS 244 GRTHLQDA PI LGQEF Y + + I + L + G TAVGTGLN E+ + Sbjct: 184 GRTHLQDATPITLGQEFSGYVAQLEQAERGIQASLPGLRQLAAGGTAVGTGLNTHAEFGA 243 Query: 245 IVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGPRA 304 V E LA P A + A + ALK + KIANDLR +ASGPR+ Sbjct: 244 RVAEKLAHGCSQPFVPAANPFAALAGHEALLFAHGALKTLAGALMKIANDLRWLASGPRS 303 Query: 305 GLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVMEPV 364 GL EI LP +PGSSIMPGKVNP E + V QVFGND+ I +G FELNV +P+ Sbjct: 304 GLGEIALPENEPGSSIMPGKVNPTQCEALTMVCAQVFGNDVAINIGGASGNFELNVFKPL 363 Query: 365 LFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAAKL 424 L N +QS ++ + +SF+ +C+ GI N ERM E +E+S+ ++TA+ PH+GYE AA + Sbjct: 364 LAHNFLQSARLLGDAMESFSRHCVVGIVPNRERMDELLERSLMLVTALAPHIGYERAAAV 423 Query: 425 AREAYLTGESIRELCIKYGVLTEEQLNEILNPYEMTHP 462 A++A+ G ++R+ + G +T E+ + + P M P Sbjct: 424 AKQAHRDGSTLRQAALALGYVTAEEFDAWVRPEAMLGP 461 Lambda K H 0.316 0.133 0.370 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: 512 Number of extensions: 17 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: 468 Length of database: 463 Length adjustment: 33 Effective length of query: 435 Effective length of database: 430 Effective search space: 187050 Effective search space used: 187050 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: 51 (24.3 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