Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate WP_104913122.1 C3B54_RS02650 class II fumarate hydratase
Query= BRENDA::Q9LCC6 (468 letters) >NCBI__GCF_002950575.1:WP_104913122.1 Length = 467 Score = 369 bits (947), Expect = e-106 Identities = 207/467 (44%), Positives = 280/467 (59%), Gaps = 12/467 (2%) Query: 4 DVRIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEV 63 D RIE D +GE +PKDA Y QT RA ENFPI+G + P I +L VKK+AA AN E+ Sbjct: 7 DFRIEHDTMGEVRVPKDALYRAQTQRAVENFPISGRGLEPGHIIALAEVKKAAASANQEL 66 Query: 64 GLLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEK 123 G+L ++ Q I+ AADEVI G + F VD Q G+GTS NMN NEV+A A E Sbjct: 67 GILSADIAQAIIHAADEVISGHHLEHFPVDTYQTGSGTSSNMNMNEVLATLASRESNES- 125 Query: 124 GNYSKISPNSHVNMSQSTNDAFPTATHIAVLS-LLNQLIETTKYMQQEFMKKADEFAGVI 182 I PN HVN SQS+ND FPT+ H+AV S L+N ++ +++ + KA +A V+ Sbjct: 126 -----IHPNDHVNASQSSNDVFPTSVHVAVTSALVNDVVPALEHLARALEDKAQAWATVV 180 Query: 183 KMGRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEY 242 K GRTHL DA P+ GQEF YAR + IERI + + ++ +G TA GTG+N + Sbjct: 181 KPGRTHLMDATPVTFGQEFSGYARQVRLGIERIHSALPRVAEVPLGGTATGTGINTPVGF 240 Query: 243 ISIVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGP 302 V LA +G PL A +A D E S AL+ ++++KIAND+R M SGP Sbjct: 241 SERVIALLATHTGLPLTEALDHFEAQGARDGLVEASGALRTIAVSLTKIANDVRWMGSGP 300 Query: 303 RAGLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVME 362 GL E+ LP QPGSSIMPGKVNPV+PE + V +V GND T+ A +G FELNV Sbjct: 301 NTGLGELALPDLQPGSSIMPGKVNPVIPEALLMVCAKVVGNDQTVAWAGASGNFELNVAI 360 Query: 363 PVLFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAA 422 PV+ +L++S ++ N ++F + + G++ N ER + E S I+T +N +GYE AA Sbjct: 361 PVMASSLLESTRLIANASRAFADKTVAGLEVNVERARALAESSPSIVTPLNRFIGYEAAA 420 Query: 423 KLAREAYLTGESIRELCI-----KYGVLTEEQLNEILNPYEMTHPGI 464 K+A+ A +IRE I + G L+EEQL+ L+ MT PG+ Sbjct: 421 KVAKHAVAEKITIREAVIALGFVERGELSEEQLDASLDVLSMTTPGL 467 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: 554 Number of extensions: 17 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: 467 Length adjustment: 33 Effective length of query: 435 Effective length of database: 434 Effective search space: 188790 Effective search space used: 188790 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