Align Aspartate ammonia-lyase; Aspartase; EC 4.3.1.1 (uncharacterized)
to candidate 15732 b1611 fumarate hydratase (NCBI)
Query= curated2:P26899 (475 letters) >FitnessBrowser__Keio:15732 Length = 467 Score = 370 bits (949), Expect = e-107 Identities = 197/463 (42%), Positives = 287/463 (61%), Gaps = 1/463 (0%) Query: 9 RVEKDFLGEKQIEADVYYGIQTLRASENFPITGYKIHEEMINALAIVKKAAALANMDVKR 68 R EKD +G + AD +G QT R+ E+F I+ K+ +I+ALA+ K+AAA N D+ Sbjct: 5 RSEKDSMGAIDVPADKLWGAQTQRSLEHFRISTEKMPTSLIHALALTKRAAAKVNEDLGL 64 Query: 69 LYEGIGQAIVQAADEILEGKWHDQFIVDPIQGGAGTSMNMNANEVIGNRALEIMGHKKGD 128 L E AI QAADE+L G+ D+F + Q G+GT NMN NEV+ NRA E++G +G Sbjct: 65 LSEEKASAIRQAADEVLAGQHDDEFPLAIWQTGSGTQSNMNMNEVLANRASELLGGVRGM 124 Query: 129 YIHLSPNTHVNMSQSTNDVFPTAIHISTLKLLEK-LLKTMEDMHSVFKQKAQEFDSVIKM 187 + PN VN SQS+NDVFPTA+H++ L L K L+ ++ + +K++ F ++K+ Sbjct: 125 ERKVHPNDDVNKSQSSNDVFPTAMHVAALLALRKQLIPQLKTLTQTLNEKSRAFADIVKI 184 Query: 188 GRTHLQDAVPIRLGQEFEAYSRVLERDIKRIKQSRQHLYEVNMGATAVGTGLNADPEYIK 247 GRTHLQDA P+ LGQE + +LE ++K I+ S H+ E+ +G TAVGTGLN PEY + Sbjct: 185 GRTHLQDATPLTLGQEISGWVAMLEHNLKHIEYSLPHVAELALGGTAVGTGLNTHPEYAR 244 Query: 248 QVVKHLADISGLPLVGADHLVDATQNTDAYTEVSASLKVCMMNMSKIANDLRLMASGPRA 307 +V LA I+ P V A + +A DA + +LK ++ KIAND+R +ASGPR Sbjct: 245 RVADELAVITCAPFVTAPNKFEALATCDALVQAHGALKGLAASLMKIANDVRWLASGPRC 304 Query: 308 GLAEISLPARQPGSSIMPGKVNPVMAELINQIAFQVIGNDNTICLASEAGQLELNVMEPV 367 G+ EIS+P +PGSSIMPGKVNP E + + QV+GND I + +G ELNV P+ Sbjct: 305 GIGEISIPENEPGSSIMPGKVNPTQCEALTMLCCQVMGNDVAINMGGASGNFELNVFRPM 364 Query: 368 LVFNLLQSISIMNNGFRSFTDNCLKGIEANEKRMKQYVEKSAGVITAVNPHLGYEAAARI 427 ++ N LQS+ ++ +G SF +C GIE N +R+ Q + +S ++TA+N H+GY+ AA I Sbjct: 365 VIHNFLQSVRLLADGMESFNKHCAVGIEPNRERINQLLNESLMLVTALNTHIGYDKAAEI 424 Query: 428 AREAIMTGQSVRDLCLQHDVLTEEELDIILNPYEMTKPGIAGK 470 A++A G +++ L L+E E D + P +M AG+ Sbjct: 425 AKKAHKEGLTLKAAALALGYLSEAEFDSWVRPEQMVGSMKAGR 467 Lambda K H 0.317 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: 466 Number of extensions: 14 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: 475 Length of database: 467 Length adjustment: 33 Effective length of query: 442 Effective length of database: 434 Effective search space: 191828 Effective search space used: 191828 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