Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate N515DRAFT_2763 N515DRAFT_2763 fumarase, class II
Query= BRENDA::Q9LCC6 (468 letters) >FitnessBrowser__Dyella79:N515DRAFT_2763 Length = 465 Score = 381 bits (978), Expect = e-110 Identities = 208/462 (45%), Positives = 290/462 (62%), Gaps = 8/462 (1%) Query: 6 RIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEVGL 65 RIE D +GE ++P DA YG QT RA +NFPI+G R+ I++LG++K +AA AN+ +G Sbjct: 5 RIEHDSMGELKVPADALYGAQTQRAVDNFPISGLRLPRAFIRALGLIKAAAAEANLGLGH 64 Query: 66 LDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEKGN 125 L K I KAA V +G+++DQF +D Q G+GTS NMNANEVIA+ A KG Sbjct: 65 LRKNQAAAIRKAALAVADGQFDDQFPIDVFQTGSGTSTNMNANEVIAHVA------GKGG 118 Query: 126 YSKISPNSHVNMSQSTNDAFPTATHI-AVLSLLNQLIETTKYMQQEFMKKADEFAGVIKM 184 +K+ PN HVN QS+ND PTA H+ A L+ QL+ K++++ ++A E V K Sbjct: 119 -AKVHPNDHVNYGQSSNDVIPTAIHVSATLTASEQLLPALKHLKKTIERRARELRNVPKT 177 Query: 185 GRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEYIS 244 GRTHL DA+P+ GQE +A IA IERI ++ + + G TAVGTG+NADP++ Sbjct: 178 GRTHLMDAMPVTFGQELSGWAAQIATAIERIEDSIKRMRRLPQGGTAVGTGINADPKFGP 237 Query: 245 IVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGPRA 304 V L K +G +A++ + D E+S LK + + KIANDLR M SGP A Sbjct: 238 AVARELKKLTGVRFDAAENYFEGMAGQDAAVELSGQLKALAVALMKIANDLRWMNSGPLA 297 Query: 305 GLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVMEPV 364 GL EI LPA QPGSSIMPGKVNPV+PE VA QV GND IT ++G F+LNVM P+ Sbjct: 298 GLGEIELPALQPGSSIMPGKVNPVIPEATAMVAAQVIGNDAAITIGGQSGNFQLNVMLPL 357 Query: 365 LFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAAKL 424 + NL+QSI ++ NV + + G K N R+KE ++K+ ++TA+NP +GYE A Sbjct: 358 IAHNLLQSIGLLANVSVLLADKAIAGFKVNAARVKEALDKNPILVTALNPVIGYEKGAAT 417 Query: 425 AREAYLTGESIRELCIKYGVLTEEQLNEILNPYEMTHPGIAG 466 A++AY I E+ ++ L++++LN++L+P +T GI G Sbjct: 418 AKQAYKQKRPIMEVALETTGLSKDELNKLLDPMALTKGGIHG 459 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: 560 Number of extensions: 28 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: 465 Length adjustment: 33 Effective length of query: 435 Effective length of database: 432 Effective search space: 187920 Effective search space used: 187920 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