Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate WP_067474702.1 BJL86_RS10470 class II fumarate hydratase
Query= BRENDA::Q9LCC6 (468 letters) >NCBI__GCF_001659785.1:WP_067474702.1 Length = 471 Score = 361 bits (927), Expect = e-104 Identities = 202/464 (43%), Positives = 283/464 (60%), Gaps = 13/464 (2%) Query: 4 DVRIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEV 63 + RIE D +GE +P +A Y QT RA ENFPI+ + I++LG++K + A N ++ Sbjct: 10 EYRIEHDTMGEVRVPVNALYRAQTQRAVENFPISFRPLERAQIRALGLLKSACASVNNDL 69 Query: 64 GLLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEK 123 GLLD E + I AA ++ +G+ + F +D Q G+GTS NMN NEVIA+ A + E Sbjct: 70 GLLDDEKARAIEAAAQKIADGEVDADFPIDVFQTGSGTSSNMNTNEVIASLAGQAGTE-- 127 Query: 124 GNYSKISPNSHVNMSQSTNDAFPTATHIAVL-SLLNQLIETTKYMQQEFMKKADEFAGVI 182 + PN HVNMSQS+ND FPTATH+A S+ LI +++ KA+E+ V+ Sbjct: 128 -----VHPNDHVNMSQSSNDTFPTATHVAAAESIAKDLIPALQHLHSALAGKAEEWKSVV 182 Query: 183 KMGRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEY 242 K GRTHL DAVP+ LGQEF YAR + IER+ + ++ +G TAVGTGLNA Y Sbjct: 183 KSGRTHLMDAVPVTLGQEFSGYARQVEAGIERLEAALPRVAELPIGGTAVGTGLNAPEGY 242 Query: 243 ISIVTEHLAKFSG-HPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASG 301 S V E L + +G + A+ +A D E S AL+ I+++KIAND+R M SG Sbjct: 243 GSAVVEKLRELTGVESISLAKDPFEAQAARDGLVEGSGALRTIAISLTKIANDVRWMGSG 302 Query: 302 PRAGLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVM 361 P GL EI LP QPGSSIMPGKVNPV+PE + QV QV GND I G FELNV Sbjct: 303 PLTGLGEIQLPDLQPGSSIMPGKVNPVLPEAVTQVGAQVIGNDAAIAWGGGNGAFELNVY 362 Query: 362 EPVLFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETA 421 P++ N ++S+ ++ NV F + C+ G+ ANE+R+K E S I+T +N +GYE A Sbjct: 363 IPMMARNFLESVKLLANVSTLFADRCISGLVANEDRLKTLAESSPSIVTPLNSAIGYEEA 422 Query: 422 AKLAREAYLTGESIRELCIKYGV----LTEEQLNEILNPYEMTH 461 AK+A++A G++IR+ + G+ L+EE+L++ L+ M + Sbjct: 423 AKVAKQALAEGKTIRQTVLDRGLVPDKLSEEELDKRLDTLAMAN 466 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: 564 Number of extensions: 32 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: 468 Length of database: 471 Length adjustment: 33 Effective length of query: 435 Effective length of database: 438 Effective search space: 190530 Effective search space used: 190530 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 24 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