Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate WP_010630565.1 RH97_RS01575 aspartate ammonia-lyase
Query= BRENDA::Q9LCC6 (468 letters) >NCBI__GCF_000246965.1:WP_010630565.1 Length = 466 Score = 407 bits (1046), Expect = e-118 Identities = 211/457 (46%), Positives = 293/457 (64%), Gaps = 1/457 (0%) Query: 5 VRIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEVG 64 +RIE D +G KE+P AYYG+ +RA ENF +T I PELI L I+KK+AA N + G Sbjct: 1 MRIETDAIGTKEVPSSAYYGIHALRAKENFNVTSETIDPELIDGLAIIKKAAASVNRKDG 60 Query: 65 LLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEKG 124 L KE I +A DEV+E K + FIV IQG AGTSINMNANEVIANRA+EL+G EKG Sbjct: 61 SLSKEKAAAIRRACDEVLERKLDHAFIVPSIQGSAGTSINMNANEVIANRAIELLGGEKG 120 Query: 125 NYSKISPNSHVNMSQSTNDAFPTATHIAVLSLLNQLIETTKYMQQEFMKKADEFAGVIKM 184 +YS I PN VN QSTND FP+A +A+L L QL +KA E ++K+ Sbjct: 121 SYSIIHPNDDVNRGQSTNDTFPSAGKLALLRLSRQLTLEIDRFIDSLDQKASELKDIVKI 180 Query: 185 GRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEYIS 244 GRT LQDA+P +G F+AYA R+++ I ++R+ L +N+G TA+GT +NA Y+ Sbjct: 181 GRTQLQDALPTTVGDTFKAYAAAAGRNLDEINHSRHGLKTLNLGGTAIGTSVNASEYYVR 240 Query: 245 IVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGPRA 304 + ++K G L A +L+DATQN D + +S A K+ + +SK+A+DLRL++SGP+ Sbjct: 241 HIVPEVSKLFGEELSQADNLIDATQNVDAFVRLSHAYKLFAVTLSKMASDLRLLSSGPQF 300 Query: 305 GLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVMEPV 364 G +E+ LP +Q GSSIMPGKVNPV+PE++NQVAFQ+ G D TIT A+EAGQ ELN EP+ Sbjct: 301 GFNELFLPKKQAGSSIMPGKVNPVIPELVNQVAFQIMGYDTTITLAAEAGQLELNAFEPI 360 Query: 365 LFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAAKL 424 + NLI + +++ +F NC+ GI+AN R + + TA+ P++GY L Sbjct: 361 IVRNLIVTSRLLSKTLVTFRINCINGIEANRPRCTDEANHCAILATALTPYIGYSKTCTL 420 Query: 425 AREAYLTGESIRELCIKYGVLTEEQLNEILNPYEMTH 461 +E+ TG I+ L + + E L ++L+P + H Sbjct: 421 VKESLQTGTPIQTLAGQLPDVPESVL-KLLDPKNLIH 456 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: 547 Number of extensions: 16 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: 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 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