Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate 8499800 DvMF_0565 aspartate ammonia-lyase (RefSeq)
Query= BRENDA::Q0PC50 (468 letters) >FitnessBrowser__Miya:8499800 Length = 521 Score = 519 bits (1336), Expect = e-151 Identities = 259/462 (56%), Positives = 341/462 (73%) Query: 1 MGTRKEHDFIGELEISDEVYYGVQTFRAVENFDISHDRLKDFPRFVRALARVKKAAAMAN 60 M R E D +GE ++ YYGVQT RA+ENFD++ + PRFV+ALA VKKAAA+AN Sbjct: 5 MEYRIERDSLGERKVPAHAYYGVQTLRALENFDVTGLTIGRHPRFVQALASVKKAAALAN 64 Query: 61 HELGLLDKNIQDAIIKACDKILEGGYYDQFVVDMIQGGAGTSTNMNANEVIANIGLELMG 120 ELGLLD ++ AI++AC ++ EG + +QFVVD+IQGGAGTS NMNANEVIAN LELMG Sbjct: 65 MELGLLDGDVGQAIVQACREVREGRFDEQFVVDIIQGGAGTSVNMNANEVIANRALELMG 124 Query: 121 HKKGEYQYLHPNDHVNLSQSTNDAYPTALHLALHDYLSDLAKAMEHLKKAYERKAEEFKD 180 +GEY + P +HVNLSQSTND YPTA +AL Y DL ++ L+ A+ K E F D Sbjct: 125 RTRGEYGVVSPLNHVNLSQSTNDVYPTAFRIALVWYARDLGVSLRELRDAFHAKGEAFAD 184 Query: 181 VLKMGRTQLQDAVPMTLGREFKTFAVMIGEDIQRVLEARKLILEINLGGTAIGTGINSHP 240 V+KM RTQLQDAVP+TLG EF + V +GEDI R+ E +L+ E+N+G TA+GTGIN+ P Sbjct: 185 VIKMARTQLQDAVPITLGAEFAAYGVTVGEDIDRLAEVARLLCEVNIGATAVGTGINTVP 244 Query: 241 DYPKVVERKIREVTGFEYTVAEDLIEATQDTGAYVQISGVLKRVATKLSKVCNDLRLLSS 300 Y +V ++ ++TG +++ +L+EAT D GAYV +SG+LKRVA KLSK+CNDLRLLSS Sbjct: 245 GYAPLVCDRLADITGLPLSLSPNLVEATSDAGAYVTLSGLLKRVAVKLSKICNDLRLLSS 304 Query: 301 GPKCGLNEINLPKMQPGSSIMPGKVNPVIPEVVNQVCYFVIGADVTVTFACEGGQLQLNV 360 GP GL EI+LP +QPGSSIMPGKVNPVIPE+VNQVC VIG D+TVT A E GQL+LNV Sbjct: 305 GPFTGLGEISLPAVQPGSSIMPGKVNPVIPELVNQVCQQVIGNDLTVTLAAEAGQLELNV 364 Query: 361 FEPVVAYSLFNSVVMLEKAMYTLADKCIDGITANEKICSDFVYNSVGIVTALNPYIGYEN 420 F P++A +LF S+ +L +A L +C++GITAN + C + ++ S+G+VTAL P IGYE Sbjct: 365 FGPIMACNLFQSLEILTRAARILRVRCVEGITANRERCLELLHGSLGMVTALAPVIGYEA 424 Query: 421 SASIAKEAMNTGKRVADIALERGLLSKEQIDEILTPSNMLNP 462 +A++ K+A TG+ D+ +ERGL+ E D+++ P+ ML P Sbjct: 425 AATVVKDARATGRTPRDLLVERGLMRSEDYDDLMDPAKMLGP 466 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: 622 Number of extensions: 17 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: 521 Length adjustment: 34 Effective length of query: 434 Effective length of database: 487 Effective search space: 211358 Effective search space used: 211358 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: 52 (24.6 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