Align Aspartate ammonia-lyase; Aspartase; EC 4.3.1.1 (uncharacterized)
to candidate 8501342 DvMF_2075 fumarate hydratase, class II (RefSeq)
Query= curated2:P26899 (475 letters) >FitnessBrowser__Miya:8501342 Length = 528 Score = 321 bits (823), Expect = 3e-92 Identities = 178/480 (37%), Positives = 278/480 (57%), Gaps = 22/480 (4%) Query: 8 YRVEKDFLGEKQIEADVYYGIQTLRASENFPITGYKIHEEMINALAIVKKAAALANMDVK 67 +R+E+D +G ++E +G QT R+ +NF I ++ +++ALA +KKAAAL N D+ Sbjct: 43 HRLERDSMGLVEVEQGRLWGAQTQRSLDNFRIGTDRMPLAVVHALARIKKAAALVNRDLG 102 Query: 68 RL------------YEGIGQAIVQAADEILEGKWHDQFIVDPIQGGAGTSMNMNANEVIG 115 L + +AI +AADE+L G+ D F + Q G+GT NMN NEV+ Sbjct: 103 LLPPPPPGQPDQPGLPHMAEAIARAADEVLAGQHDDHFPLSVWQTGSGTQTNMNVNEVLA 162 Query: 116 NRALEIMGHK-----KGDYIHLSP----NTHVNMSQSTNDVFPTAIHIST-LKLLEKLLK 165 NRA +++ G + H+ P N HVN QS+ND FP A+H++ L L + LL Sbjct: 163 NRATQLLAEAAHAAASGGHPHIHPPIHPNDHVNRCQSSNDAFPAAMHLAAALALRDDLLP 222 Query: 166 TMEDMHSVFKQKAQEFDSVIKMGRTHLQDAVPIRLGQEFEAYSRVLERDIKRIKQSRQHL 225 + + + KA ++K+GRTHLQDAVP+ LG E ++ L+ ++ + + HL Sbjct: 223 GVRHLRDALRAKAAACADIVKIGRTHLQDAVPLTLGDEMSGWAAQLDACLEGLDAAMPHL 282 Query: 226 YEVNMGATAVGTGLNADPEYIKQVVKHLADISGLPLVGADHLVDATQNTDAYTEVSASLK 285 + +G TAVGTGLNA P + + + LAD++GLPLV A + A D S +L+ Sbjct: 283 CRLALGGTAVGTGLNAHPAFAPRAIALLADMTGLPLVPAPNPFAALAAHDGLVLTSGALR 342 Query: 286 VCMMNMSKIANDLRLMASGPRAGLAEISLPARQPGSSIMPGKVNPVMAELINQIAFQVIG 345 + KIAND+R +ASGPR G+ E+ LP +PGSSIMPGKVNP E + +A QV+G Sbjct: 343 ALATALLKIANDVRWLASGPRCGIGELRLPENEPGSSIMPGKVNPTQCEALTMVAVQVMG 402 Query: 346 NDNTICLASEAGQLELNVMEPVLVFNLLQSISIMNNGFRSFTDNCLKGIEANEKRMKQYV 405 D + +A G ELNV +P+++ N+L S+ ++ +G RSF D+ + G++ + + +V Sbjct: 403 LDVAVGMAGSQGNFELNVFKPLIIHNVLTSMRLLADGCRSFADHAVAGMQPDRAGIAAHV 462 Query: 406 EKSAGVITAVNPHLGYEAAARIAREAIMTGQSVRDLCLQHDVLTEEELDIILNPYEMTKP 465 +S ++TA+ P +GY+ AA+ A A G ++R+ CL+ +L D ++P M +P Sbjct: 463 GRSLMLVTALAPVVGYDRAAQAAHRAHAQGITLREACLEMQLLDGAAFDAAVDPLRMARP 522 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: 573 Number of extensions: 25 Number of successful extensions: 6 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: 528 Length adjustment: 34 Effective length of query: 441 Effective length of database: 494 Effective search space: 217854 Effective search space used: 217854 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: 52 (24.6 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