Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate WP_085544376.1 B9Y55_RS05550 class II fumarate hydratase
Query= BRENDA::Q9LCC6 (468 letters) >NCBI__GCF_900177735.1:WP_085544376.1 Length = 453 Score = 369 bits (947), Expect = e-106 Identities = 195/455 (42%), Positives = 291/455 (63%), Gaps = 7/455 (1%) Query: 6 RIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEVGL 65 R+E+D LGE ++P+ A +G QT R+ NFPI ++ E+I+++G++KK+AA+ N+E+ + Sbjct: 4 RVERDSLGEVQVPEQALWGAQTQRSLVNFPIGTEKMPSEVIEAVGMIKKAAAIVNVELKV 63 Query: 66 LDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEKGN 125 LDKE G I +AAD+VI G +DQF + Q G+GT NMN NEV+AN A + GE Sbjct: 64 LDKEKGVAIARAADKVIAGDHDDQFPLSLWQTGSGTQTNMNVNEVLANLASKYSGEP--- 120 Query: 126 YSKISPNSHVNMSQSTNDAFPTATHIA-VLSLLNQLIETTKYMQQEFMKKADEFAGVIKM 184 I PN HVN SQS+ND FPTA H+A VL++ +LI + M +K D +AG++K+ Sbjct: 121 ---IHPNDHVNRSQSSNDVFPTAMHLATVLAVEERLIPAMEGMAGVLGEKRDRYAGLVKI 177 Query: 185 GRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEYIS 244 GRTHLQDA P+ LGQE + R+I R I + L D+ +G TAVGTGLNA + Sbjct: 178 GRTHLQDATPVTLGQEIGGWLRMIERCQSMIMTSVEYLKDLAIGGTAVGTGLNAPDGFGE 237 Query: 245 IVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGPRA 304 V L +G RSA + + D + LK ++ KIAND+R +ASGPR Sbjct: 238 KVAVQLGDITGIDFRSAPDKFHSLTSKDELVALHGTLKALAADLMKIANDVRWLASGPRC 297 Query: 305 GLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVMEPV 364 GL E+V+PA +PGSSIMPGKVNP E + ++ QV GND + A+ G F+LNV PV Sbjct: 298 GLGELVIPANEPGSSIMPGKVNPTQVEAITMISVQVMGNDAVVGIAASQGNFQLNVFMPV 357 Query: 365 LFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAAKL 424 + ++QS+ ++++ SFTE CLKG++A+EER+ ++S+ ++TA+ P +GY+TAA + Sbjct: 358 MINAVLQSVRLLSDGINSFTERCLKGLEADEERLSSTRDRSLMLVTALAPALGYDTAASV 417 Query: 425 AREAYLTGESIRELCIKYGVLTEEQLNEILNPYEM 459 A++A+ +++E + GVLT ++ ++++ P M Sbjct: 418 AKKAHQERTTLKEAAVSMGVLTGDEFDKLVVPERM 452 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: 518 Number of extensions: 23 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: 453 Length adjustment: 33 Effective length of query: 435 Effective length of database: 420 Effective search space: 182700 Effective search space used: 182700 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