Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate 209008 DVU0080 fumarate hydratase, class II
Query= BRENDA::Q9LCC6 (468 letters) >MicrobesOnline__882:209008 Length = 468 Score = 366 bits (939), Expect = e-105 Identities = 188/463 (40%), Positives = 285/463 (61%), Gaps = 1/463 (0%) Query: 1 MNTDVRIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALAN 60 M VRIE D +G E+P D Y+G QT RA E+F I R+ E++++LG++K++AA N Sbjct: 2 MTPAVRIEHDSMGAVEVPADRYWGAQTQRALEHFRIGTERMPQEMVQALGLIKRAAAETN 61 Query: 61 MEVGLLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMG 120 + LL ++ + +AA EV G + F + Q G+GT NMN NEV+ANRA EL+G Sbjct: 62 AALELLPRQTADAVARAATEVASGALPNHFPLCVWQTGSGTQTNMNVNEVVANRACELLG 121 Query: 121 EEKGNYSKISPNSHVNMSQSTNDAFPTATHIAV-LSLLNQLIETTKYMQQEFMKKADEFA 179 +G+ + PN HVN+ QS+ND FP A HIA L L + L+ + + ++ E +A EFA Sbjct: 122 GVRGDRKLVHPNDHVNLCQSSNDVFPAAMHIAAALGLRSMLLPSLQALEAELEARAHEFA 181 Query: 180 GVIKMGRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNAD 239 G++K+GRTHLQDAVP+ LGQEF YA +A ++ L + +G TAVGTGLNA Sbjct: 182 GLVKVGRTHLQDAVPLTLGQEFSGYAAQLALCRRQLEGMMPLLCALALGGTAVGTGLNAH 241 Query: 240 PEYISIVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMA 299 PE+ LA ++G P + A + S AL+ + + K+ ND+RL+A Sbjct: 242 PEFARRAVARLAGYTGLPFLPVDNPFAALAGHEALVAYSGALRTLAVALFKVGNDIRLLA 301 Query: 300 SGPRAGLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELN 359 SGPR G+ E+ LPA +PGSSIMPGKVNP E + VA QV G D + A G ELN Sbjct: 302 SGPRCGIGELELPANEPGSSIMPGKVNPTQCEALTMVAVQVMGLDNAVGIAGSQGHLELN 361 Query: 360 VMEPVLFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYE 419 V +P++ N+++S ++ + +SF + ++G++A ER+ +V++S+ ++TA++ HVGY+ Sbjct: 362 VFKPLIARNVLESARLLADSMRSFRMHAVRGLRAVPERIASHVDRSLMLVTALSRHVGYD 421 Query: 420 TAAKLAREAYLTGESIRELCIKYGVLTEEQLNEILNPYEMTHP 462 AA++A A+ G ++RE C++ G++ E + ++P M HP Sbjct: 422 RAAEVAHLAHAEGLTLREACLRLGLMDGEAFDRAVDPVRMAHP 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: 502 Number of extensions: 19 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: 468 Length adjustment: 33 Effective length of query: 435 Effective length of database: 435 Effective search space: 189225 Effective search space used: 189225 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