Align Aspartate ammonia-lyase; Aspartase; EC 4.3.1.1 (uncharacterized)
to candidate GFF848 PS417_04305 aspartate ammonia-lyase
Query= curated2:P26899 (475 letters) >FitnessBrowser__WCS417:GFF848 Length = 458 Score = 363 bits (933), Expect = e-105 Identities = 194/460 (42%), Positives = 283/460 (61%), Gaps = 7/460 (1%) Query: 9 RVEKDFLGEKQIEADVYYGIQTLRASENFPITGYKIHEEMINALAIVKKAAALANMDVKR 68 R+E+D +GE Q+ A+ YG QT RA NFPI+ ++ + I AL + K AAA N+D+K+ Sbjct: 5 RIERDSMGELQVPAEALYGAQTQRAVNNFPISHQRMPAQFIRALILAKTAAAKVNVDLKQ 64 Query: 69 LYEGIGQAIVQAADEILEGKWHDQFIVDPIQGGAGTSMNMNANEVIGNRALEIMGHKKGD 128 + EG G+AIV AA +LEG + F VD Q G+GTS NMNANEVI A ++G Sbjct: 65 ISEGQGKAIVDAAQGLLEGDFMRHFPVDIFQTGSGTSSNMNANEVIATLATRLLGES--- 121 Query: 129 YIHLSPNTHVNMSQSTNDVFPTAIHIST-LKLLEKLLKTMEDMHSVFKQKAQEFDSVIKM 187 ++PN HVN QS+ND+ PT IH+S L L E+ L + + V +QKA+E IK Sbjct: 122 ---VNPNDHVNCGQSSNDIIPTTIHVSAALVLHEQTLPALLHLVQVIEQKAEEVHPFIKT 178 Query: 188 GRTHLQDAVPIRLGQEFEAYSRVLERDIKRIKQSRQHLYEVNMGATAVGTGLNADPEYIK 247 GRTHL DA+P+R+ Q +S+ L+ +I ++ L + G TAVGTG+NA PE+ Sbjct: 179 GRTHLMDAMPVRMSQVLNGWSQQLKANIGHLQDLLPSLQALAQGGTAVGTGINAHPEFAV 238 Query: 248 QVVKHLADISGLPLVGADHLVDATQNTDAYTEVSASLKVCMMNMSKIANDLRLMASGPRA 307 + + L+ ++G+ +L + D VS LK +++ KIANDLR M SGP A Sbjct: 239 RFSQQLSSLTGVKFTPGKNLFALIGSQDTAVAVSGQLKAIAVSLMKIANDLRWMNSGPLA 298 Query: 308 GLAEISLPARQPGSSIMPGKVNPVMAELINQIAFQVIGNDNTICLASEAGQLELNVMEPV 367 GL EI L QPGSSIMPGKVNPV+ E +A QVIGND I +A ++G ELNVM P+ Sbjct: 299 GLGEIELEGLQPGSSIMPGKVNPVIPEATAMVAAQVIGNDAVITVAGQSGNFELNVMLPI 358 Query: 368 LVFNLLQSISIMNNGFRSFTDNCLKGIEANEKRMKQYVEKSAGVITAVNPHLGYEAAARI 427 + NLL S+ ++ N R D + + NE ++K+ + ++ ++TA+NP +GY+ AA I Sbjct: 359 IAQNLLSSLELLANASRLLADKAIASFKVNEAKLKEALSRNPILVTALNPIIGYQKAAEI 418 Query: 428 AREAIMTGQSVRDLCLQHDVLTEEELDIILNPYEMTKPGI 467 A++A G+ V D+ L+H L +L+++L+P ++T G+ Sbjct: 419 AKKAYQQGRPVIDVALEHTDLPRSQLEVLLDPEKLTAGGV 458 Lambda K H 0.317 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: 510 Number of extensions: 25 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: 475 Length of database: 458 Length adjustment: 33 Effective length of query: 442 Effective length of database: 425 Effective search space: 187850 Effective search space used: 187850 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