Align Aspartate ammonia-lyase; Aspartase; EC 4.3.1.1 (uncharacterized)
to candidate CA265_RS23855 CA265_RS23855 fumarate hydratase, class II
Query= curated2:P56149 (468 letters) >FitnessBrowser__Pedo557:CA265_RS23855 Length = 465 Score = 394 bits (1013), Expect = e-114 Identities = 212/459 (46%), Positives = 297/459 (64%), Gaps = 3/459 (0%) Query: 2 RIEHDFIGQMEISDEVYYGIQTLRASENFFITNDKLCSYPVFIKSFAQVKKAATLANVQL 61 RIEHD +G++++ + Y+G QT R+ NF I + + I +F +KKAA LAN +L Sbjct: 4 RIEHDTMGEVQVPADKYWGAQTERSRNNFKIGPEGSMPKEI-IHAFGYLKKAAALANTEL 62 Query: 62 GLIDEKLKIAICHACDLLIDGKYHDQFIVDMIQGGAGTSTNMNMNEVIANLALEYMGHQK 121 G++ + I ACD +I G+ DQF + + Q G+GT +NMN NEVIAN A G Sbjct: 63 GVLSAEKAGLIAKACDEIIAGQLDDQFPLVIWQTGSGTQSNMNGNEVIANRAHVINGGSL 122 Query: 122 GE-YQFCHPNDHVNRSQSTNDAYPSALKIAIYE-RLSNLVAPMKALRDAFAQKAKEFAHV 179 + + HPND VN+SQS+ND YP+A+ IA Y+ + N + ++ LR+ AQK +EF+ + Sbjct: 123 ADDKKVLHPNDDVNKSQSSNDTYPTAMHIAAYKLTVENTIPGLEKLRNTLAQKVEEFSTI 182 Query: 180 IKMGRTQLQDAVPMTLGQEFETYALMVDRDIEQVLDARNWVRELNLGGTAIGTGINSHPD 239 +K GRT DA P+TLGQEF Y +D I + +A V EL LGGTA+GTG+N+ Sbjct: 183 VKTGRTHFMDATPLTLGQEFSGYVQQIDNSIRAIKNALVMVAELALGGTAVGTGLNTPKG 242 Query: 240 YRSLIEKKIQEVTGRPFVMANNLIEATQSTGAYVQVSGVLKRIAVKLSKVCNDLRLLSSG 299 Y L+ KKI ++TG PFV A N EA + A V++SG LKR AV L KV ND+R+LSSG Sbjct: 243 YDVLVAKKIADLTGLPFVTAPNKFEALAAHDAMVELSGALKRTAVALMKVANDVRMLSSG 302 Query: 300 PRAGLNEINLPKMQPGSSIMPGKVNPVIPEVVNQVCFAVIGNDLSVALAAEGGQLQLNVF 359 PR G+ EI +P +PGSSIMPGKVNP PE + VC VIGND++V++ G +LNVF Sbjct: 303 PRCGIGEIVIPDNEPGSSIMPGKVNPTQPEALTMVCAQVIGNDVAVSVGGMSGHFELNVF 362 Query: 360 EPVIAYKLFHSFVILGRAIETLTTKCVEGITANEKICHDYVFNSIGIVTALNPHIGYEKS 419 +P+IA + S ++G A + T KC EGITAN ++ NS+ +VTALNPH+GYE + Sbjct: 363 KPLIAANVLQSARLIGDACVSFTDKCAEGITANLPEIEKHLQNSLMLVTALNPHVGYENA 422 Query: 420 AMIAKEALKSDRSIYDIALEKKILTKEQLDDIFKPENML 458 A IAK+A K ++++ A+E +LT EQ D+ +PE+M+ Sbjct: 423 AKIAKKAHKENKTLKAAAVELGLLTNEQFDEWVRPEDMV 461 Lambda K H 0.320 0.135 0.388 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: 511 Number of extensions: 21 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: 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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