Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate Ga0059261_1040 Ga0059261_1040 fumarase, class II (EC 4.2.1.2)
Query= BRENDA::Q9HTD7 (474 letters) >FitnessBrowser__Korea:Ga0059261_1040 Length = 463 Score = 342 bits (877), Expect = 2e-98 Identities = 197/463 (42%), Positives = 277/463 (59%), Gaps = 3/463 (0%) Query: 4 VASSRIEKDLLGTLEVPADAYYGIQTLRAVNNFRLSGVPLSHYPKLVVALAMVKQAAADA 63 V +R E D +G +EVPADAY+G QT R++ NF G+ +V A A+VKQAAA Sbjct: 1 VTQTRTETDSIGAIEVPADAYWGAQTQRSIENFPF-GLTERMPIGIVRAQAIVKQAAARV 59 Query: 64 NRQLGHLPEDKHAAISEACARLIRGDFHEQFVVDMIQGGAGTSTNMNANEVIANIALEAM 123 N + G PE AAI +A ++ G+ +QF + + Q G+GT TNMN NEVIA A E + Sbjct: 60 NAKHGLKPEIV-AAIEDAAQAIVSGELDDQFPLVIWQTGSGTQTNMNVNEVIAGFANEKL 118 Query: 124 GHTKGEYKYLHPNNDVNMAQSTNDAYPTAIRLGLLLG-HDTLLASLDSLIQAFAAKGVEF 182 T+G +HPN+ VNM+QS+ND++PTA+ + +L D LL +L L + AAK + Sbjct: 119 AGTRGGKTPVHPNDHVNMSQSSNDSFPTALHVATVLATRDALLPALGQLTASLAAKAEAW 178 Query: 183 AGVLKMGRTQLQDAVPMTLGQEFHAFATTLGEDLDRLRRLAPELLTEVNLGGTAIGTGIN 242 ++K+GRT QDA P+TLGQEF +A L R+ + ++ +GGTA+GTG+N Sbjct: 179 DHIVKIGRTHTQDATPLTLGQEFSGYAAQLVSCRARIEGALNGSIRKLAIGGTAVGTGLN 238 Query: 243 ADPGYQKLAVERLAAISGQPLKPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDLRL 302 A G+ + ++ I+G + A + E + V FSG L AV L+KI ND+R Sbjct: 239 APEGWAEDMTAAISDITGTEFQNAPNKFEQLAAKDGLVFFSGALNTLAVALNKIANDIRF 298 Query: 303 LSSGPRTGINEINLPPRQPGSSIMPGKVNPVIPEAVNQVAFEVIGNDLALTLAAEGGQLQ 362 L SGPR+G+ E++LP +PGSSIMPGKVNP E++ VA +VIGN+ A+T+ G + Sbjct: 299 LGSGPRSGLGELSLPANEPGSSIMPGKVNPTQAESLTMVAAQVIGNNQAVTVGGMQGHFE 358 Query: 363 LNVMEPLIAYKIFDSIRLLQRAMDMLREHCITGITANVERCHELVEHSIGLVTALNPYIG 422 LNV PLI + SI LL M E C+ GI AN + +LV S+ LVTAL P IG Sbjct: 359 LNVFMPLIGANVLRSIHLLSVGMTSFAERCVDGIEANERQIADLVGRSLMLVTALAPEIG 418 Query: 423 YENSTRIAKTALESGRGVLELVREEKLLDEATLADILLPENMI 465 Y+N+ +IAK A G + E + L+DEAT ++ PE M+ Sbjct: 419 YDNAAKIAKVAHAEGLTLREAGLKLGLVDEATFDRLVRPETMV 461 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: 507 Number of extensions: 21 Number of successful extensions: 4 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: 463 Length adjustment: 33 Effective length of query: 441 Effective length of database: 430 Effective search space: 189630 Effective search space used: 189630 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