Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate H281DRAFT_00025 H281DRAFT_00025 fumarase, class II
Query= BRENDA::Q9LCC6 (468 letters) >FitnessBrowser__Burk376:H281DRAFT_00025 Length = 490 Score = 356 bits (914), Expect = e-103 Identities = 186/465 (40%), Positives = 282/465 (60%), Gaps = 1/465 (0%) Query: 3 TDVRIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANME 62 T R E D +G E+P D Y+G QT R+ ++F I R+ + + GIVKK+AAL N + Sbjct: 25 TGKRKEFDSMGTVEVPADRYWGSQTARSLQHFSIGDDRMPKAVYHAYGIVKKAAALVNAD 84 Query: 63 VGLLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEE 122 G L K I++AADEVI GK +D F + Q G+GT NMN NEV++NRA++L+ E Sbjct: 85 AGRLPKWKADAIIRAADEVIAGKLDDHFPLFVWQTGSGTQSNMNVNEVVSNRAIQLLDGE 144 Query: 123 KGNYSKISPNSHVNMSQSTNDAFPTATHIAVLSLLNQ-LIETTKYMQQEFMKKADEFAGV 181 G I PN VNM QS+ND+FP+A H+A +SL+++ L+ + + +KA + V Sbjct: 145 LGTQQPIGPNDDVNMGQSSNDSFPSAMHVAAVSLIDERLVPELSKLAEAIEEKAQGWMDV 204 Query: 182 IKMGRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPE 241 IK+GRTHLQDA P+ +GQE+ +A + I + R LY++ +G TAVGTGLNA Sbjct: 205 IKVGRTHLQDATPLSVGQEWSGWAAQLRAVIAEVERCREGLYELALGGTAVGTGLNAPKN 264 Query: 242 YISIVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASG 301 + V + +A+ +G P +A + A + D S+A + + + KIAND+R +ASG Sbjct: 265 FSLNVAKQIAQLTGKPFVTAPNKFMAQGSLDAMVRASAANRGAAVALMKIANDMRWLASG 324 Query: 302 PRAGLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVM 361 PR GL E+ LPA +PGSSIMPGKVNP E M +A QV G D I A G FELN M Sbjct: 325 PRCGLGELKLPANEPGSSIMPGKVNPTQCEAMVMIAIQVIGEDTAIAFAGSQGNFELNAM 384 Query: 362 EPVLFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETA 421 P++ N + S +I+ + + F ++G + E++K Y++ ++ ++TA++P +GY+ A Sbjct: 385 RPIIINNFLHSATILADGAEKFRRFSVEGTALDREQIKRYLDNNLMLVTALSPVIGYQNA 444 Query: 422 AKLAREAYLTGESIRELCIKYGVLTEEQLNEILNPYEMTHPGIAG 466 A +A A + +++E ++ G + E+Q ++I+ P M G+AG Sbjct: 445 AHIAESAQASDSTLKEAALQSGEIDEQQYDKIIVPRNMVGNGVAG 489 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: 498 Number of extensions: 16 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: 490 Length adjustment: 34 Effective length of query: 434 Effective length of database: 456 Effective search space: 197904 Effective search space used: 197904 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