Align Aspartate ammonia-lyase; Aspartase; EC 4.3.1.1 (uncharacterized)
to candidate GFF3190 HP15_3132 fumarate hydratase class II
Query= curated2:P26899 (475 letters) >FitnessBrowser__Marino:GFF3190 Length = 458 Score = 355 bits (910), Expect = e-102 Identities = 200/463 (43%), Positives = 279/463 (60%), Gaps = 8/463 (1%) Query: 7 EYRVEKDFLGEKQIEADVYYGIQTLRASENFPITGYKIHEEMINALAIVKKAAALANMDV 66 E+R E D LG+ Q+ AD +G QT RA ENFP++G + + I A+A +K+AAA AN + Sbjct: 3 EFRTETDSLGDVQVPADALWGAQTQRAVENFPVSGQPMPQPFIAAVAQIKRAAAEANTSL 62 Query: 67 KRLYEGIGQAIVQAADEILEGKWHDQFIVDPIQGGAGTSMNMNANEVIGNRALEIMGHKK 126 L + AI QA +++++G++ DQF VD Q G+GTS NMN NEVI + A Sbjct: 63 GLLDNDLRDAISQACEDLVKGEYADQFPVDRYQTGSGTSTNMNVNEVIASIA-----RNA 117 Query: 127 GDYIHLSPNTHVNMSQSTNDVFPTAIHIST-LKLLEKLLKTMEDMHSVFKQKAQEFDSVI 185 G +H PN HVNMSQS+NDV PTAIH+S + EKLL + + V ++ F S + Sbjct: 118 GFEVH--PNDHVNMSQSSNDVIPTAIHVSAVIAAKEKLLPALSHLCGVIYEQEAAFSSQV 175 Query: 186 KMGRTHLQDAVPIRLGQEFEAYSRVLERDIKRIKQSRQHLYEVNMGATAVGTGLNADPEY 245 K GRTHL DA+P+ LGQE + + L KR++ + L V G TAVGTG+NA PE+ Sbjct: 176 KTGRTHLMDAMPVTLGQELKTWREQLLAVEKRVEAAADELLAVPQGGTAVGTGINALPEF 235 Query: 246 IKQVVKHLADISGLPLVGADHLVDATQNTDAYTEVSASLKVCMMNMSKIANDLRLMASGP 305 Q VK L +G P DH DA +SA L+ + ++KIANDLR M SGP Sbjct: 236 PGQFVKFLRANTGYPFTSLDHKFTGQSAVDAPVALSAQLRGAAIVLTKIANDLRWMNSGP 295 Query: 306 RAGLAEISLPARQPGSSIMPGKVNPVMAELINQIAFQVIGNDNTICLASEAGQLELNVME 365 GLAEISLPA QPGSSIMPGKVNPV+ E + + QV+G D+ + +A ++G +LNVM Sbjct: 296 IHGLAEISLPALQPGSSIMPGKVNPVIPESVAMVGAQVMGLDSAVAIAGQSGNFQLNVML 355 Query: 366 PVLVFNLLQSISIMNNGFRSFTDNCLKGIEANEKRMKQYVEKSAGVITAVNPHLGYEAAA 425 P++ NLL ++ N D +K N + V K+ ++TA+NP +GY AA Sbjct: 356 PLVGGNLLDMTDLLANAAIMLADKAIKDFTVNADNLNAGVGKNPVLVTALNPEIGYSLAA 415 Query: 426 RIAREAIMTGQSVRDLCLQHDVLTEEELDIILNPYEMTKPGIA 468 IA+EA TG+ V D+ + L+ E L+ +++P ++T+ GIA Sbjct: 416 DIAKEAYKTGRPVIDVAEERSGLSRERLEELMDPLKLTRGGIA 458 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: 502 Number of extensions: 28 Number of successful extensions: 3 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: 458 Length adjustment: 33 Effective length of query: 442 Effective length of database: 425 Effective search space: 187850 Effective search space used: 187850 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