Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate Synpcc7942_1007 Synpcc7942_1007 fumarate hydratase
Query= BRENDA::Q9LCC6 (468 letters) >FitnessBrowser__SynE:Synpcc7942_1007 Length = 463 Score = 366 bits (940), Expect = e-106 Identities = 185/455 (40%), Positives = 290/455 (63%), Gaps = 1/455 (0%) Query: 6 RIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEVGL 65 R E D +GE +P D Y+G QT R+ F I R+ E+ +L I KK++ALAN ++G+ Sbjct: 8 RRESDSMGEVLVPTDRYWGAQTQRSLHYFSIGQDRMPIEVCHALAIAKKASALANRDLGV 67 Query: 66 LDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEKGN 125 L E I +AADE+I G+ +D F + G+GT NMN NEVIANRA+E+ G G+ Sbjct: 68 LSAEKADLIAQAADEIIAGQLDDHFPLYVWMTGSGTQANMNVNEVIANRAIEMAGGVLGS 127 Query: 126 YSKISPNSHVNMSQSTNDAFPTATHIAVLSLLN-QLIETTKYMQQEFMKKADEFAGVIKM 184 + I PN VN SQS+ND FPTA HIA + QL+ + + ++Q K DE+ G++K+ Sbjct: 128 KTPIHPNDDVNRSQSSNDVFPTAMHIAAAQAIGRQLLPSIERLEQSLQAKVDEWQGIVKI 187 Query: 185 GRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEYIS 244 GRTHLQDAVP+ LGQEF + ++A + +R+ N LY + +G TAVGTGLNA + Sbjct: 188 GRTHLQDAVPLTLGQEFSGFVAMLAENRQRLHNALQELYPLALGGTAVGTGLNAPTGFDV 247 Query: 245 IVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGPRA 304 V +++A+ +G P +A + D + +S +L+ +++ KIAND+RL+A GPR Sbjct: 248 AVADYIAQLTGLPFVTATNKFAQIGAHDAFVALSGSLRGLAVSLYKIANDIRLLACGPRC 307 Query: 305 GLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVMEPV 364 G +E+ LPA +PGSSIMPGKVNP E + VA QV G D + A +G ELNV +P+ Sbjct: 308 GFNELSLPANEPGSSIMPGKVNPTQCEALAMVAVQVMGYDAAVAFAGASGYLELNVYKPL 367 Query: 365 LFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAAKL 424 + +N+++SI I+++ +F ++G+ AN +++ Y+E+S+ ++TA+ P +GY+ AAK+ Sbjct: 368 MVYNVLESIRILSDASDNFRRFTVEGMTANTDQINTYLERSLMLVTALTPAIGYDQAAKV 427 Query: 425 AREAYLTGESIRELCIKYGVLTEEQLNEILNPYEM 459 A+ A+ S++E C++ G ++ E+ + ++P ++ Sbjct: 428 AKYAFEKNLSLKEACLELGCISSEEFDRWVDPAQL 462 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: 528 Number of extensions: 29 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: 468 Length of database: 463 Length adjustment: 33 Effective length of query: 435 Effective length of database: 430 Effective search space: 187050 Effective search space used: 187050 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