Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate RR42_RS33090 RR42_RS33090 fumarate hydratase
Query= BRENDA::Q9LCC6 (468 letters) >FitnessBrowser__Cup4G11:RR42_RS33090 Length = 467 Score = 376 bits (965), Expect = e-108 Identities = 192/460 (41%), Positives = 290/460 (63%), Gaps = 3/460 (0%) Query: 6 RIEKDFLGEKEIPKDAYYGVQTIRATENFPI--TGYRIHPELIKSLGIVKKSAALANMEV 63 R E D +G ++P D Y+G QT R+T NFPI + +R +I++LGI+K++AA AN E+ Sbjct: 5 RSETDSMGAIDVPADRYWGAQTQRSTINFPIGVSRFRWQRPVIRALGILKRAAAEANAEL 64 Query: 64 GLLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEK 123 G L ++G+ IV+AADEVI GK ++ F + Q G+GT NMNANEVI+NRA+E+ G E Sbjct: 65 GELPPDIGRLIVQAADEVISGKLDEHFPLVVFQTGSGTQSNMNANEVISNRAIEIAGGEL 124 Query: 124 GNYSKISPNSHVNMSQSTNDAFPTATHIAVLSLLN-QLIETTKYMQQEFMKKADEFAGVI 182 G+ + N HVN QS+ND FPTA HIAV+ ++ +L+ ++ KA + ++ Sbjct: 125 GSKKPVHSNDHVNRGQSSNDTFPTAMHIAVVEQIHTKLLPAVGALRDTLAAKAQAYQDIV 184 Query: 183 KMGRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEY 242 K GRTHLQDA PI LGQE A+ I + + L ++ +G TAVGTGLNA P++ Sbjct: 185 KTGRTHLQDATPITLGQEISAWVAQIDFGLNAVKTAEPGLLELAIGGTAVGTGLNAHPQF 244 Query: 243 ISIVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGP 302 + ++A +GHP A + A D + S+AL+ + K+AND+R +ASGP Sbjct: 245 GARAAAYIAALTGHPFVDAPNKFFALSAHDALVQTSAALRTLSGGLMKMANDVRWLASGP 304 Query: 303 RAGLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVME 362 R G+ E+ +P +PGSSIMPGKVNP E M V QVFGND T+ A G F+LNV + Sbjct: 305 RCGIGELNIPENEPGSSIMPGKVNPTQCEAMTMVCAQVFGNDATVAFAGSQGNFQLNVYK 364 Query: 363 PVLFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAA 422 PV+ N+++SI ++ + +F ++C GI+ N ++ E ++K++ ++TA+N H+GY+ AA Sbjct: 365 PVMVHNVLESIELIADACLAFNDHCALGIEPNLPKIAENLDKNLMLVTALNRHIGYDKAA 424 Query: 423 KLAREAYLTGESIRELCIKYGVLTEEQLNEILNPYEMTHP 462 +A++A+ G +++ + G LTE++ + P EMTHP Sbjct: 425 AIAKKAHKEGLTLKAAALALGYLTEDEYARWIVPIEMTHP 464 Lambda K H 0.316 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: 525 Number of extensions: 23 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: 468 Length of database: 467 Length adjustment: 33 Effective length of query: 435 Effective length of database: 434 Effective search space: 188790 Effective search space used: 188790 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