Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate WP_013431069.1 CALKRO_RS10910 aspartate ammonia-lyase
Query= BRENDA::Q9LCC6 (468 letters) >NCBI__GCF_000166775.1:WP_013431069.1 Length = 461 Score = 432 bits (1111), Expect = e-125 Identities = 225/453 (49%), Positives = 306/453 (67%) Query: 6 RIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEVGL 65 RIEKDFLG E+ YG+ T RA NF ++G + +LIK+ +VKK+ A+AN EVGL Sbjct: 3 RIEKDFLGSIELSDIELYGIHTKRAFANFNVSGKSVDKDLIKAFVMVKKACAIANYEVGL 62 Query: 66 LDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEKGN 125 LD+++ IV A DE++ GK++DQFIVD QGGAGTS NMN NEVIAN AL +G + G Sbjct: 63 LDEKIKDAIVFACDEILAGKYDDQFIVDRFQGGAGTSTNMNVNEVIANVALTHIGRKPGE 122 Query: 126 YSKISPNSHVNMSQSTNDAFPTATHIAVLSLLNQLIETTKYMQQEFMKKADEFAGVIKMG 185 Y I P +HVNMSQSTND +PTA IA + + +L E +Q+ KK EF VIK G Sbjct: 123 YDIIHPINHVNMSQSTNDVYPTALRIATIWNVRELSEECAELQKSLQKKEHEFEDVIKAG 182 Query: 186 RTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEYISI 245 RT LQDA+P+ LGQEF AYA+ I+RD R+ L +N+GATAVGTG+NA +YI Sbjct: 183 RTQLQDALPVTLGQEFGAYAQAISRDRWRLYKVEERLRVVNLGATAVGTGVNAPLKYIFK 242 Query: 246 VTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGPRAG 305 V E L + L + +L+DATQN D + E S LK +N+SKIANDLRL++SGP G Sbjct: 243 VIEILRNLTKIGLARSDYLMDATQNADVFVECSGLLKALAVNLSKIANDLRLLSSGPNTG 302 Query: 306 LSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVMEPVL 365 L+EI +PA Q GSSIMPGKVNPV+PE++N VAFQV ND IT A++AGQ ELN P++ Sbjct: 303 LNEINMPAVQAGSSIMPGKVNPVIPELINTVAFQVMANDFAITLAAQAGQLELNAFLPLI 362 Query: 366 FFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAAKLA 425 NL++S+ I+ N K F + C+ GI AN+E+ EY +K+ I ++ +GY+ AA++A Sbjct: 363 ANNLLESLKILKNGIKIFRQQCIDGITANKEKCLEYAKKTPAIAASLIDRIGYDKAAEIA 422 Query: 426 REAYLTGESIRELCIKYGVLTEEQLNEILNPYE 458 ++A L + I ++ + ++ E++ E+LNP+E Sbjct: 423 KKAILENKQIIDVVKELNIMDEKEAQELLNPFE 455 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: 582 Number of extensions: 24 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: 461 Length adjustment: 33 Effective length of query: 435 Effective length of database: 428 Effective search space: 186180 Effective search space used: 186180 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