Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate WP_010960815.1 MCA_RS07605 class II fumarate hydratase
Query= BRENDA::Q9LCC6 (468 letters) >NCBI__GCF_000008325.1:WP_010960815.1 Length = 469 Score = 362 bits (929), Expect = e-104 Identities = 196/464 (42%), Positives = 275/464 (59%), Gaps = 7/464 (1%) Query: 4 DVRIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEV 63 D RIEKD +GE +P A Y QT RA +NFP++G + P I+++ +K+ AA N+ + Sbjct: 5 DYRIEKDSMGELRVPVSALYAAQTQRAIDNFPVSGLALPPAFIRAIARIKQCAARVNVAL 64 Query: 64 GLLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEK 123 G LD G+ I+ AA+E+I G + DQF VD Q G+GTS NMN NEV+A A G Sbjct: 65 GHLDAGKGEAIMAAAEEIIGGAYADQFPVDVFQTGSGTSTNMNVNEVLATLASRRAG--- 121 Query: 124 GNYSKISPNSHVNMSQSTNDAFPTATHI-AVLSLLNQLIETTKYMQQEFMKKADEFAGVI 182 + +S N VNM QS+ND PTA H+ A L++ LI +++ K + Sbjct: 122 ---TPVSANDDVNMGQSSNDVIPTAIHVSAALAVNEHLIPALEHLAATIRYKGLAHPKAV 178 Query: 183 KMGRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEY 242 K GRTHL DA+P+ L QE +A +A ++R+ + LY + G TAVGTG+NADP + Sbjct: 179 KTGRTHLMDAMPVRLEQELSGWALQVANGVDRLRASLPRLYKLGQGGTAVGTGINADPAF 238 Query: 243 ISIVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGP 302 S E LA +G P R ++ D E+S LK + + KIANDLR M SGP Sbjct: 239 ASSFAEALADATGLPFRPNDSFFESLSCQDAAVELSGQLKTIAVGIMKIANDLRWMNSGP 298 Query: 303 RAGLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVME 362 AGL EI LPA QPGSSIMPGKVNPV+PE VA QV GND IT A ++G F+LNVM Sbjct: 299 LAGLGEIELPALQPGSSIMPGKVNPVIPEAACMVAAQVIGNDAAITVAGQSGSFQLNVML 358 Query: 363 PVLFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAA 422 PV+ +NL+QSI ++ N+ + + + + E+ ++ + + ++TA+NP +GY AA Sbjct: 359 PVIAYNLLQSIELLANIARLLADKAIADFRVREDNLRRALATNPILVTALNPVIGYLKAA 418 Query: 423 KLAREAYLTGESIRELCIKYGVLTEEQLNEILNPYEMTHPGIAG 466 ++A+ AY TG I E+ I+ L +L +L+P +T GI G Sbjct: 419 EIAKTAYRTGRPILEVAIEMSGLDRAELERLLDPAALTTGGIHG 462 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: 543 Number of extensions: 32 Number of successful extensions: 3 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: 469 Length adjustment: 33 Effective length of query: 435 Effective length of database: 436 Effective search space: 189660 Effective search space used: 189660 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 24 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