Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate 207337 DVU1871 aspartate ammonia-lyase
Query= BRENDA::Q0PC50 (468 letters) >MicrobesOnline__882:207337 Length = 468 Score = 540 bits (1390), Expect = e-158 Identities = 270/462 (58%), Positives = 345/462 (74%) Query: 1 MGTRKEHDFIGELEISDEVYYGVQTFRAVENFDISHDRLKDFPRFVRALARVKKAAAMAN 60 M R E D +GE + VYYGVQT RA+ENF I+ + FPRF++ALA VKKAAA+AN Sbjct: 1 MEYRTERDSLGEKRVPAGVYYGVQTLRALENFQITAMPVATFPRFIQALAAVKKAAALAN 60 Query: 61 HELGLLDKNIQDAIIKACDKILEGGYYDQFVVDMIQGGAGTSTNMNANEVIANIGLELMG 120 ELGLLD + +AI+ AC + G + DQF VD+IQGGAGTS NMNANEVIAN LEL+G Sbjct: 61 MELGLLDAGVGEAIVNACRDVRAGRFDDQFPVDVIQGGAGTSVNMNANEVIANRALELLG 120 Query: 121 HKKGEYQYLHPNDHVNLSQSTNDAYPTALHLALHDYLSDLAKAMEHLKKAYERKAEEFKD 180 H KG Y+ + P +HVNLSQSTND YPTAL +AL Y +L+ A+ L+ A++ K +EF Sbjct: 121 HPKGRYEVISPLNHVNLSQSTNDVYPTALRIALVWYARELSTALRDLRAAFDAKGDEFAG 180 Query: 181 VLKMGRTQLQDAVPMTLGREFKTFAVMIGEDIQRVLEARKLILEINLGGTAIGTGINSHP 240 V+KM RTQLQDAVP+TLG EF + V IGEDI R+ +A +L+ E+N+G TA+GTGINS P Sbjct: 181 VIKMARTQLQDAVPITLGAEFAAWGVTIGEDIDRLDDAARLLCEVNIGATAVGTGINSVP 240 Query: 241 DYPKVVERKIREVTGFEYTVAEDLIEATQDTGAYVQISGVLKRVATKLSKVCNDLRLLSS 300 Y +V ++ ++ G A +L+EAT D GAYV +SG+LKRVA KLSK+CNDLRLL+S Sbjct: 241 GYASLVRERLADICGLPLVTAANLVEATSDAGAYVMLSGLLKRVAVKLSKICNDLRLLAS 300 Query: 301 GPKCGLNEINLPKMQPGSSIMPGKVNPVIPEVVNQVCYFVIGADVTVTFACEGGQLQLNV 360 GP GL+EINLP MQPGSSIMPGKVNPVIPEVVNQVCY VIG D+TVTFA EGGQL+LNV Sbjct: 301 GPFTGLHEINLPPMQPGSSIMPGKVNPVIPEVVNQVCYQVIGNDLTVTFAAEGGQLELNV 360 Query: 361 FEPVVAYSLFNSVVMLEKAMYTLADKCIDGITANEKICSDFVYNSVGIVTALNPYIGYEN 420 F PV+A +LF S+ ML KA TL ++C+ GITAN + C + V +S+G+VTAL P IGYE Sbjct: 361 FLPVIALNLFQSLQMLTKASRTLRERCVVGITANPERCLELVRHSLGVVTALAPVIGYET 420 Query: 421 SASIAKEAMNTGKRVADIALERGLLSKEQIDEILTPSNMLNP 462 +A +AKEA +G+ V ++ G+++ E+ +E+L P+ ML+P Sbjct: 421 AARLAKEAQESGRSVPEVLQAEGIMTPEEFEELLDPAKMLSP 462 Lambda K H 0.318 0.135 0.383 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: 558 Number of extensions: 9 Number of successful extensions: 1 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 (21.7 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