Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate 5207534 Shew_0068 fumarate lyase (RefSeq)
Query= BRENDA::Q9HTD7 (474 letters) >FitnessBrowser__PV4:5207534 Length = 459 Score = 315 bits (807), Expect = 2e-90 Identities = 180/460 (39%), Positives = 265/460 (57%), Gaps = 11/460 (2%) Query: 7 SRIEKDLLGTLEVPADAYYGIQTLRAVNNFRLSGVPLSHYPKLVVALAMVKQAAADANRQ 66 S+ D +G L +PADA YG QT RA+ NF +SG P+ + AL + K AA +AN Sbjct: 3 SKAVSDSMGDLNIPADALYGAQTARAIKNFPVSGRPMPR--SFIRALLLAKLAAVEANVA 60 Query: 67 LGHLPEDKHAAISEACARLIRG-DFHEQFVVDMIQGGAGTSTNMNANEVIANIALEAMGH 125 L LP + A+++A L+ F +DM Q G+GTS+NMNANEV+A + +++G Sbjct: 61 LRLLPPNIAPAVAQAVQELLADPQMMRHFPIDMFQTGSGTSSNMNANEVLATLVSKSLGQ 120 Query: 126 TKGEYKYLHPNNDVNMAQSTNDAYPTAIRLGLLLG-HDTLLASLDSLIQAFAAKGVEFAG 184 +HPN+ +N+ QS+ND P+ I + LL +LL SL L Q K + A Sbjct: 121 A------VHPNDVINLGQSSNDIIPSTIHISALLAVEQSLLPSLTLLSQTITTKAQQLAD 174 Query: 185 VLKMGRTQLQDAVPMTLGQEFHAFATTLGEDLDRLRRLAPELLTEVNLGGTAIGTGINAD 244 V K GRT L DA+P+ Q +A+ + + +R+ + L ++ +GGTA+GTG+N Sbjct: 175 VTKTGRTHLMDAMPVRFDQVLGGWASQIDDCRERIASQG-DALAQLPVGGTAVGTGVNTH 233 Query: 245 PGYQKLAVERLAAISGQPLKPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDLRLLS 304 + +L ERL+A++ +PA +L + V SG LK AV + KI NDLR ++ Sbjct: 234 EEFSRLFCERLSALTRTQFRPADNLFSRMASHDTAVALSGQLKTLAVAIMKISNDLRWMN 293 Query: 305 SGPRTGINEINLPPRQPGSSIMPGKVNPVIPEAVNQVAFEVIGNDLALTLAAEGGQLQLN 364 SGP G+ EI+L P QPGSSIMPGKVNPVIPE+ VA +V+G D+A+T+A + G +LN Sbjct: 294 SGPLAGLGEISLQPLQPGSSIMPGKVNPVIPESACMVAAQVMGKDMAITIAGQSGNFELN 353 Query: 365 VMEPLIAYKIFDSIRLLQRAMDMLREHCITGITANVERCHELVEHSIGLVTALNPYIGYE 424 VM+PLIA + +SI +L +L + I N + + + + LVTAL+P +GY Sbjct: 354 VMQPLIAVNLLESIEILSNVSRLLADKAIASFVVNRGKIADSLHRNPILVTALSPKVGYV 413 Query: 425 NSTRIAKTALESGRGVLELVREEKLLDEATLADILLPENM 464 + +I K A + R +LE+ E L E L +L PE + Sbjct: 414 QAAKIVKQAYQEQRPILEVAMELTDLSEEELRRLLDPERL 453 Lambda K H 0.318 0.135 0.380 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: 25 Number of successful extensions: 5 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: 474 Length of database: 459 Length adjustment: 33 Effective length of query: 441 Effective length of database: 426 Effective search space: 187866 Effective search space used: 187866 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 (21.7 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