Align Aspartate ammonia-lyase; Aspartase; EC 4.3.1.1 (uncharacterized)
to candidate GFF3751 PS417_19200 fumarate hydratase
Query= curated2:P26899 (475 letters) >FitnessBrowser__WCS417:GFF3751 Length = 460 Score = 353 bits (905), Expect = e-102 Identities = 190/455 (41%), Positives = 285/455 (62%), Gaps = 1/455 (0%) Query: 9 RVEKDFLGEKQIEADVYYGIQTLRASENFPITGYKIHEEMINALAIVKKAAALANMDVKR 68 R+E D LGE + D Y+G QT R+ NF I ++ +++ALA+VKKAAA N Sbjct: 3 RIETDSLGEVHVPDDAYWGAQTQRSLVNFAIGEQRMPLAVLHALALVKKAAARVNDRNGD 62 Query: 69 LYEGIGQAIVQAADEILEGKWHDQFIVDPIQGGAGTSMNMNANEVIGNRALEIMGHKKGD 128 L I + I QAADE+L G+ DQF + Q G+GT NMNANEVI RA E+ G+++G Sbjct: 63 LPADIARLIEQAADEVLAGQHDDQFPLVVWQTGSGTQSNMNANEVIAGRANELAGNQRGG 122 Query: 129 YIHLSPNTHVNMSQSTNDVFPTAIHISTLKLL-EKLLKTMEDMHSVFKQKAQEFDSVIKM 187 + PN HVN SQS+ND FPTA+ I+ ++ + ++LL + + ++A + ++K Sbjct: 123 KSPVHPNDHVNRSQSSNDCFPTAMSIAAVQAVHQRLLPAIATLSGGLAEQAAKHMKLVKT 182 Query: 188 GRTHLQDAVPIRLGQEFEAYSRVLERDIKRIKQSRQHLYEVNMGATAVGTGLNADPEYIK 247 GRTH+ DA PI GQE A+ L+ + I+ + + E+ G TAVGTGLNA + + Sbjct: 183 GRTHMMDATPITFGQELSAFIAQLDYAERAIRAALPAVCELAQGGTAVGTGLNAPHGFGE 242 Query: 248 QVVKHLADISGLPLVGADHLVDATQNTDAYTEVSASLKVCMMNMSKIANDLRLMASGPRA 307 + LA +SGLP V A + A + + +LK + + KIANDLRL+ SGPR Sbjct: 243 AIASELAALSGLPFVTAPNKFAALSGHEPLVTLHGALKTLAVALMKIANDLRLLGSGPRT 302 Query: 308 GLAEISLPARQPGSSIMPGKVNPVMAELINQIAFQVIGNDNTICLASEAGQLELNVMEPV 367 GLAE+ LPA +PGSSIMPGKVNP E ++ +A QV+GND TI +A+ G L+LNV +PV Sbjct: 303 GLAEVKLPANEPGSSIMPGKVNPTQCEALSMLACQVLGNDVTIGIAASQGHLQLNVYKPV 362 Query: 368 LVFNLLQSISIMNNGFRSFTDNCLKGIEANEKRMKQYVEKSAGVITAVNPHLGYEAAARI 427 ++ NLL+SI ++ +G +F ++C+ G+E + +M +++E+ ++TA+NPH+GY+ +A I Sbjct: 363 IIHNLLESIRLLADGCNNFQEHCVAGLEPDPLQMAEHLERGLMLVTALNPHIGYDKSAEI 422 Query: 428 AREAIMTGQSVRDLCLQHDVLTEEELDIILNPYEM 462 A++A G ++R+ L LT+ E D + P +M Sbjct: 423 AKKAYAEGLTLREAALDLGYLTDAEFDQWVRPEDM 457 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: 467 Number of extensions: 17 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: 460 Length adjustment: 33 Effective length of query: 442 Effective length of database: 427 Effective search space: 188734 Effective search space used: 188734 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