Align Aspartate ammonia-lyase; Aspartase; EC 4.3.1.1 (uncharacterized)
to candidate BWI76_RS16270 BWI76_RS16270 fumarate hydratase, class II
Query= curated2:P26899 (475 letters) >FitnessBrowser__Koxy:BWI76_RS16270 Length = 466 Score = 377 bits (969), Expect = e-109 Identities = 199/456 (43%), Positives = 283/456 (62%), Gaps = 1/456 (0%) Query: 8 YRVEKDFLGEKQIEADVYYGIQTLRASENFPITGYKIHEEMINALAIVKKAAALANMDVK 67 YR EKD +G + AD +G QT R+ E+F I+ K+ E+I+ALA+ K+AAA N D+ Sbjct: 4 YRSEKDSMGAIDVPADKLWGAQTQRSLEHFRISTEKMPVELIHALALTKRAAAKVNNDLG 63 Query: 68 RLYEGIGQAIVQAADEILEGKWHDQFIVDPIQGGAGTSMNMNANEVIGNRALEIMGHKKG 127 L QAI+QAADE+L G+ D F + Q G+GT NMN NEV+ NRA E++G +G Sbjct: 64 LLAAEKAQAIIQAADEVLAGQHPDAFPLAIWQTGSGTQSNMNMNEVLANRASELLGGARG 123 Query: 128 DYIHLSPNTHVNMSQSTNDVFPTAIHISTL-KLLEKLLKTMEDMHSVFKQKAQEFDSVIK 186 + PN VN SQS+NDVFPTA+H++ + L EKL+ + + KA F ++K Sbjct: 124 MERKVHPNDDVNKSQSSNDVFPTAMHVAAIIALREKLIPQLNVLKQTLNDKAVAFSDIVK 183 Query: 187 MGRTHLQDAVPIRLGQEFEAYSRVLERDIKRIKQSRQHLYEVNMGATAVGTGLNADPEYI 246 +GRTHLQDA P+ LGQE + +LE ++K I S HL E+ +G TAVGTGLN P+Y Sbjct: 184 IGRTHLQDATPLTLGQEISGWVAMLEHNLKHIDHSLPHLAELALGGTAVGTGLNTHPQYA 243 Query: 247 KQVVKHLADISGLPLVGADHLVDATQNTDAYTEVSASLKVCMMNMSKIANDLRLMASGPR 306 +V LA +SG P V A + +A DA +LK ++ KIAND+R +ASGPR Sbjct: 244 VRVAAELAALSGQPFVTAPNKFEALATVDALVHAHGALKGLAASLMKIANDVRWLASGPR 303 Query: 307 AGLAEISLPARQPGSSIMPGKVNPVMAELINQIAFQVIGNDNTICLASEAGQLELNVMEP 366 G+ EI++P +PGSSIMPGKVNP E + + QV+GND + + +G ELNV P Sbjct: 304 CGIGEIAIPENEPGSSIMPGKVNPTQCEALTMLCCQVMGNDVAVNIGGASGNFELNVYRP 363 Query: 367 VLVFNLLQSISIMNNGFRSFTDNCLKGIEANEKRMKQYVEKSAGVITAVNPHLGYEAAAR 426 +++ N LQS+ ++ G SF ++C GIE N +R+ Q + +S ++TA+N H+GY+ AA Sbjct: 364 LVIHNFLQSVRLLAEGMASFNEHCAVGIEPNRERISQLLNESLMLVTALNTHIGYDKAAE 423 Query: 427 IAREAIMTGQSVRDLCLQHDVLTEEELDIILNPYEM 462 IA++A G +++ L LTE+E D + P EM Sbjct: 424 IAKKAHKEGLTLKASALALGYLTEDEFDRWVRPQEM 459 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: 471 Number of extensions: 11 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: 466 Length adjustment: 33 Effective length of query: 442 Effective length of database: 433 Effective search space: 191386 Effective search space used: 191386 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