Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate 207231 DVU1766 aspartate ammonia-lyase, putative
Query= BRENDA::Q9LCC6 (468 letters) >MicrobesOnline__882:207231 Length = 470 Score = 372 bits (956), Expect = e-107 Identities = 193/462 (41%), Positives = 279/462 (60%) Query: 5 VRIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEVG 64 +RIE D LG+ +P+ A +G T RA N ++G +HPE+I++ G VK++ A NM +G Sbjct: 9 IRIEHDLLGDCAVPRTALHGAHTQRALSNVALSGRPLHPEIIRAFGAVKRACARTNMNLG 68 Query: 65 LLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEKG 124 L +EV + I+ A DE+ +G + +VD +QGGAGTS NMN NEV+ANRA E++G +G Sbjct: 69 HLSREVAEAIIMACDELEDGGLGEHIVVDALQGGAGTSANMNVNEVLANRAEEMLGGTRG 128 Query: 125 NYSKISPNSHVNMSQSTNDAFPTATHIAVLSLLNQLIETTKYMQQEFMKKADEFAGVIKM 184 Y + P +HVN+ QSTND FPTA IA L LL +L +Q F FA V+++ Sbjct: 129 QYQLVDPLAHVNLHQSTNDVFPTAVRIAALRLLARLEPAIAALQSAFQTHEASFAQVVRL 188 Query: 185 GRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEYIS 244 GRT LQDAVP+ G A+A ++RD R+ L +N+G TA+GTG+ A YI Sbjct: 189 GRTQLQDAVPMTFGAACGAWAEALSRDRWRVFKCSERLRVVNLGGTAIGTGIAAPRSYIL 248 Query: 245 IVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGPRA 304 V + L + +G PL A++L+DATQN D + EVS LK N+ K+++DLRL+ASGP Sbjct: 249 SVVDRLREDTGLPLARAENLMDATQNVDAFVEVSGILKAHASNLLKLSSDLRLLASGPGG 308 Query: 305 GLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVMEPV 364 G+ E+VLP Q GSSIMPGKVNPV+ E + Q A Q NDL IT +++ GQ ELN P+ Sbjct: 309 GIGEVVLPPVQAGSSIMPGKVNPVVCETVAQAAMQATANDLAITLSAQHGQLELNAFMPL 368 Query: 365 LFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAAKL 424 + L+ I ++TN F C++G+ + E +V S +TA+ P +GY A+++ Sbjct: 369 IADALLHGIELLTNACDLFRTRCVEGLHPDTETCARHVSTSTATLTALVPEIGYAAASEM 428 Query: 425 AREAYLTGESIRELCIKYGVLTEEQLNEILNPYEMTHPGIAG 466 AR G + G++ E++L +L+P + G G Sbjct: 429 ARHMREHGTDVFGAAKATGLIDEDRLARLLSPERLVALGYRG 470 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: 505 Number of extensions: 17 Number of successful extensions: 1 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: 470 Length adjustment: 33 Effective length of query: 435 Effective length of database: 437 Effective search space: 190095 Effective search space used: 190095 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