Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate RR42_RS37365 RR42_RS37365 fumarate hydratase
Query= BRENDA::Q9LCC6 (468 letters) >FitnessBrowser__Cup4G11:RR42_RS37365 Length = 468 Score = 349 bits (896), Expect = e-100 Identities = 186/456 (40%), Positives = 271/456 (59%), Gaps = 1/456 (0%) Query: 6 RIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEVGL 65 RIE D LG+ +P +G QT R+ +NF I + P LI++ I+K AA AN + + Sbjct: 10 RIETDSLGDIPVPARHLWGAQTERSRQNFRIGCETMPPALIEAFAILKLCAARANRALHV 69 Query: 66 LDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEKGN 125 L E+ I AA E+I GKW +F + Q G+GT NMN NEVIANRA++L+G E G Sbjct: 70 LKPELAHAIEAAAQEIIAGKWPGEFPLSVWQTGSGTQTNMNLNEVIANRAIQLLGGEPGA 129 Query: 126 YSKISPNSHVNMSQSTNDAFPTATHIAVLSLLN-QLIETTKYMQQEFMKKADEFAGVIKM 184 + PN HVN SQS+ND+FPTA HIA + QL+ + +QQ +K D F ++K+ Sbjct: 130 KQPVHPNDHVNASQSSNDSFPTAMHIAATRAIQLQLLPALERLQQALGRKVDAFGDIVKV 189 Query: 185 GRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEYIS 244 GRTHLQDAVP+ LGQEF Y + R+ + G TAVGTGLNA + + Sbjct: 190 GRTHLQDAVPLTLGQEFSGYEAQVGDAQSRLRQAMLRAMPVPQGGTAVGTGLNAPHGFAA 249 Query: 245 IVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGPRA 304 L+ ++G P A + + D ++S AL + KIA D L+ SGPRA Sbjct: 250 AFARALSDYTGLPFEPAPNRYALQASHDALADLSGALNTTASSFLKIARDFMLLGSGPRA 309 Query: 305 GLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVMEPV 364 G +E++LPA +PGSSIMPGKVNP E + V +V GN T+T A+ G ELN +PV Sbjct: 310 GFAELILPANEPGSSIMPGKVNPTQAEALAMVCCRVIGNHTTVTLANGLGTLELNAYKPV 369 Query: 365 LFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAAKL 424 + ++L+QS++++ + SF E ++G++A+ ER+ E + +S+ +TA+NPH+GY+ AA++ Sbjct: 370 IIYSLLQSVTLLADAAASFAERMVQGVQADRERIAEMLGRSLMPVTALNPHLGYDRAAEI 429 Query: 425 AREAYLTGESIRELCIKYGVLTEEQLNEILNPYEMT 460 AR A G +RE + G +T Q + ++ +MT Sbjct: 430 ARLALTRGLPLREAALASGHVTAAQFDAWVDLKDMT 465 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: 486 Number of extensions: 19 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: 468 Length adjustment: 33 Effective length of query: 435 Effective length of database: 435 Effective search space: 189225 Effective search space used: 189225 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