Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate WP_010631085.1 RH97_RS04205 class II fumarate hydratase
Query= BRENDA::Q9LCC6 (468 letters) >NCBI__GCF_000246965.1:WP_010631085.1 Length = 462 Score = 387 bits (995), Expect = e-112 Identities = 198/458 (43%), Positives = 298/458 (65%), Gaps = 2/458 (0%) Query: 6 RIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEVGL 65 RIE D +GE ++P D + QT R+ NF I R+ LI++ ++KK AALAN E+G Sbjct: 4 RIEHDTMGEVKVPADRLWAAQTERSRNNFQIGWERMPIGLIRAFAVLKKGAALANRELGK 63 Query: 66 LDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEKGN 125 LD++ I ++ADEV+ GKW+D+F + Q G+GT NMN NEVIA+RA +++ +EKG+ Sbjct: 64 LDEDKASAISRSADEVLSGKWDDEFPLVVWQTGSGTQSNMNMNEVIASRANQIL-KEKGS 122 Query: 126 YSKISPNSHVNMSQSTNDAFPTATHIAVLSLL-NQLIETTKYMQQEFMKKADEFAGVIKM 184 + PN VN SQS+ND FPTA HIA L+ + ++++ +++QQ +K++ F ++K+ Sbjct: 123 DLHVHPNDDVNKSQSSNDTFPTALHIAALTAVEDEVLPALRHLQQTLEQKSEAFRDIVKI 182 Query: 185 GRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEYIS 244 GRTHLQDA P+ LGQE +A ++ R I ++ N L D+ +G TAVGTGLNA P++ Sbjct: 183 GRTHLQDATPLTLGQEISGWAYMLDRSEAMIRSSSNYLRDLAIGGTAVGTGLNAHPDFGR 242 Query: 245 IVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGPRA 304 E +++ +G S+ + A + D V ALK ++ KIAND+R +ASGPR Sbjct: 243 QAAEKISEITGKKFISSPNKFQALTSHDQIVTVHGALKALAADLMKIANDVRWLASGPRC 302 Query: 305 GLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVMEPV 364 G+ E+ +PA +PGSSIMPGKVNP E + VA QV GND I A+ G FELNV +PV Sbjct: 303 GIGELTIPANEPGSSIMPGKVNPTQCEAVTMVAVQVMGNDAAIGFAASQGNFELNVFKPV 362 Query: 365 LFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAAKL 424 + +N +QS ++ +V KSF ++C GIK E++ E + S+ ++TA+NP++GYE AAK+ Sbjct: 363 IGYNFLQSARLLADVMKSFDQHCAAGIKPVREKINENLHHSLMLVTALNPYIGYEQAAKI 422 Query: 425 AREAYLTGESIRELCIKYGVLTEEQLNEILNPYEMTHP 462 ++ A+ G S++E +K +LT EQ ++ + P +MT P Sbjct: 423 SKTAFKEGLSLKEAAVKLKILTAEQFDQYVRPEKMTGP 460 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: 19 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: 462 Length adjustment: 33 Effective length of query: 435 Effective length of database: 429 Effective search space: 186615 Effective search space used: 186615 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