Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate Echvi_1329 Echvi_1329 fumarate hydratase, class II
Query= BRENDA::Q9LCC6 (468 letters) >FitnessBrowser__Cola:Echvi_1329 Length = 466 Score = 377 bits (968), Expect = e-109 Identities = 199/461 (43%), Positives = 286/461 (62%), Gaps = 10/461 (2%) Query: 6 RIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYR--IHPELIKSLGIVKKSAALANMEV 63 R+EKD +G E+P D Y+G QT R+ NF I G R + E+ + I+KKSAAL N E+ Sbjct: 4 RVEKDTMGPVEVPADKYWGAQTQRSINNFKIGGERNRMPLEITHAFAILKKSAALTNAEL 63 Query: 64 GLLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEK 123 G+L +E I K DE++EGK +DQF + Q G+GT NMNANEVIA R L G Sbjct: 64 GVLPQEKADAIAKVCDEIVEGKLDDQFPLVIWQTGSGTQSNMNANEVIAYRGHVLGGGSL 123 Query: 124 GNYSK-ISPNSHVNMSQSTNDAFPTATHIAVLSLLNQLIETT----KYMQQEFMKKADEF 178 + K I PN VN SQS+ND FPTA HIA ++ +ETT + ++ K+D+F Sbjct: 124 EDEQKTIHPNDDVNKSQSSNDTFPTAMHIAAYKMV---VETTIPGVEKLRDTLKDKSDQF 180 Query: 179 AGVIKMGRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNA 238 V+K+GRTH DA P+ LGQEF Y + + + NT +L ++ +G TAVGTGLN Sbjct: 181 MDVVKIGRTHFMDATPLTLGQEFSGYVAQLNHGLRALKNTLEHLSELALGGTAVGTGLNT 240 Query: 239 DPEYISIVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLM 298 Y +V + +A+FSGHP +A + ++ D E ALK +++ KIAND+R++ Sbjct: 241 PKGYAELVAKKIAEFSGHPFVTAPNKFESLAAHDAIVETHGALKQLAVSLMKIANDIRML 300 Query: 299 ASGPRAGLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFEL 358 +SGPR+G+ EI++P +PGSSIMPGKVNP E M V QV GND ++ G FEL Sbjct: 301 SSGPRSGIGEILIPENEPGSSIMPGKVNPTQAEAMTMVCAQVIGNDTAVSVGGSNGHFEL 360 Query: 359 NVMEPVLFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGY 418 NV +P++ NL+ S ++ + SF +NC+ GI+ N +K+++E S+ ++TA+N H+GY Sbjct: 361 NVFKPMMIHNLLTSARLLGDACVSFHDNCVIGIEPNRPFIKKHLENSLMLVTALNTHIGY 420 Query: 419 ETAAKLAREAYLTGESIRELCIKYGVLTEEQLNEILNPYEM 459 E AA +A++A+ G S+RE I +LT EQ +E + P +M Sbjct: 421 ENAAAIAKKAHKEGTSLREAAIDLELLTSEQFDEWVKPEDM 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: 526 Number of extensions: 13 Number of successful extensions: 4 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: 466 Length adjustment: 33 Effective length of query: 435 Effective length of database: 433 Effective search space: 188355 Effective search space used: 188355 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