Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate 3608944 Dshi_2334 fumarate hydratase, class II (RefSeq)
Query= BRENDA::Q9LCC6 (468 letters) >FitnessBrowser__Dino:3608944 Length = 465 Score = 383 bits (983), Expect = e-111 Identities = 194/461 (42%), Positives = 287/461 (62%), Gaps = 1/461 (0%) Query: 3 TDVRIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANME 62 T+ R E D G E+P D Y+G QT R+ NFPI + ++++LG++KK+ A+AN + Sbjct: 4 TETRTETDSFGPLEVPADKYWGAQTQRSIMNFPIGWEKQPVAIVRALGVIKKACAMANKK 63 Query: 63 VGLLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEE 122 G LD + I++AA EVI+GK++D F + Q G+GT NMN+NEVIANRA+E++G Sbjct: 64 SGKLDARLADAIIQAAGEVIDGKFDDNFPLVVWQTGSGTQSNMNSNEVIANRAIEILGGV 123 Query: 123 KGNYSKISPNSHVNMSQSTNDAFPTATHIAVLSLLNQ-LIETTKYMQQEFMKKADEFAGV 181 G+ + PN H NM QS+ND FPTA HIA + L+ + + KA+EF + Sbjct: 124 IGSKDPVHPNDHCNMGQSSNDTFPTAMHIAAATTARDVLLPGLVKLAEGLEAKAEEFKDI 183 Query: 182 IKMGRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPE 241 IK+GRTH QDA P+ LGQEF YA+ I I RI +Y++ G TAVGTGLN P Sbjct: 184 IKIGRTHTQDATPLTLGQEFSGYAKQIRNGIARIEMALPGIYELAQGGTAVGTGLNTSPG 243 Query: 242 YISIVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASG 301 + V ++A+ +G P +A + +A D +S A+K + KIAND+R + SG Sbjct: 244 WSETVAANMAEITGLPFVTAPNKFEALAAHDAMVFMSGAIKTTAMAAYKIANDMRFLGSG 303 Query: 302 PRAGLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVM 361 PR+GL E++LP +PGSSIMPGKVNP E M QV + GND I+ A G FELNV Sbjct: 304 PRSGLGELILPENEPGSSIMPGKVNPTQAEAMTQVCAHILGNDAAISFAGSQGHFELNVY 363 Query: 362 EPVLFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETA 421 P++ +NL+QS++++ + SFTE L G +ANEER+ + +++S+ ++TA+ P +GY+ A Sbjct: 364 NPMMSYNLLQSMTLLGDAADSFTERMLMGTRANEERIDKLMKESLMLVTALAPTIGYDNA 423 Query: 422 AKLAREAYLTGESIRELCIKYGVLTEEQLNEILNPYEMTHP 462 K+A+ A+ G +++E I G + E ++++ P +M P Sbjct: 424 TKVAKTAHKNGTTLKEEAIALGFVDAETFDKVVRPEDMIGP 464 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: 534 Number of extensions: 20 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: 465 Length adjustment: 33 Effective length of query: 435 Effective length of database: 432 Effective search space: 187920 Effective search space used: 187920 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