Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate WP_011386008.1 AMB_RS18480 class II fumarate hydratase
Query= BRENDA::Q9LCC6 (468 letters) >NCBI__GCF_000009985.1:WP_011386008.1 Length = 460 Score = 353 bits (907), Expect = e-102 Identities = 187/452 (41%), Positives = 277/452 (61%), Gaps = 1/452 (0%) Query: 6 RIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEVGL 65 R EKD G ++P+ +G QT R+ E F I+G R+ ELI +L VK A AN E+GL Sbjct: 5 RPEKDSFGIIQVPEPHIWGAQTQRSLEYFAISGERMPMELISALARVKGGCARANAELGL 64 Query: 66 LDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEKGN 125 L I+ AA EV+ G+ ++F + Q G+GT NMN NEV+ANRA E++G E+G Sbjct: 65 LAAGKADAIIAAAQEVLSGRHGEEFPLSVWQTGSGTQTNMNMNEVLANRASEILGGERGL 124 Query: 126 YSKISPNSHVNMSQSTNDAFPTATHIAV-LSLLNQLIETTKYMQQEFMKKADEFAGVIKM 184 + N VN+ QS+ND FPTA H+A ++++ L+ + ++++ + +EFA ++K+ Sbjct: 125 NRCVHANDDVNLGQSSNDVFPTAMHVAAAVTVVTGLLPSLAHLRKTLVGLTEEFAAIVKI 184 Query: 185 GRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEYIS 244 GRTHLQDA P+ LGQEF YA + + T +LY + +G TAVGTGLN PE+ + Sbjct: 185 GRTHLQDATPLTLGQEFSGYAAQLDHAEAVLLATLPSLYPLAIGGTAVGTGLNTHPEFGA 244 Query: 245 IVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGPRA 304 V LA G P SA + A D + A+K + KIAND+R +ASGPR Sbjct: 245 RVAAQLAADLGLPFVSATNKFAALAAHDGMVAMHGAVKTLAAALMKIANDIRWLASGPRC 304 Query: 305 GLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVMEPV 364 GL EI LP +PGSSIMPGKVNP E + QV GND+ IT +G FELNV +P+ Sbjct: 305 GLGEISLPENEPGSSIMPGKVNPTQCEALTMACCQVMGNDVAITMGGASGNFELNVFKPL 364 Query: 365 LFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAAKL 424 + N +QS+ +M + SF +C++GI AN +R+ + +E+S+ ++TA+ PH+GY+ AA++ Sbjct: 365 IAHNFLQSVRLMADGMASFERHCVRGITANRQRIDQLLEQSLMLVTALAPHIGYDRAAEI 424 Query: 425 AREAYLTGESIRELCIKYGVLTEEQLNEILNP 456 A+ A+ G ++R+ + G +T EQ + ++P Sbjct: 425 AKSAHAGGATLRQAALATGYVTAEQFDVWVDP 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: 504 Number of extensions: 20 Number of successful extensions: 2 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: 460 Length adjustment: 33 Effective length of query: 435 Effective length of database: 427 Effective search space: 185745 Effective search space used: 185745 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