Align Aspartate ammonia-lyase; Aspartase; EC 4.3.1.1 (uncharacterized)
to candidate PfGW456L13_5022 Fumarate hydratase class II (EC 4.2.1.2)
Query= curated2:P26899 (475 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5022 Length = 458 Score = 362 bits (929), Expect = e-104 Identities = 194/460 (42%), Positives = 284/460 (61%), Gaps = 7/460 (1%) Query: 9 RVEKDFLGEKQIEADVYYGIQTLRASENFPITGYKIHEEMINALAIVKKAAALANMDVKR 68 R+E+D +GE Q+ D YG QT RA +NFPI+G + + I AL + K AAA N+++K+ Sbjct: 5 RIERDSMGELQVPEDALYGAQTQRAVDNFPISGKPMPVQFIRALILAKAAAARTNVELKQ 64 Query: 69 LYEGIGQAIVQAADEILEGKWHDQFIVDPIQGGAGTSMNMNANEVIGNRALEIMGHKKGD 128 + E G+AIV AA +LEG + F VD Q G+GTS NMNANEVI A ++G Sbjct: 65 IGEAQGKAIVDAAQGLLEGDFMQHFPVDVFQTGSGTSSNMNANEVIATLASRLLGEA--- 121 Query: 129 YIHLSPNTHVNMSQSTNDVFPTAIHIST-LKLLEKLLKTMEDMHSVFKQKAQEFDSVIKM 187 ++PN HVN QS+ND+ PT IH+S L L E+LL + + V ++KA++ +K Sbjct: 122 ---VNPNDHVNCGQSSNDIIPTTIHVSAALALHEQLLPALTHLVQVIERKAEQVHHHVKT 178 Query: 188 GRTHLQDAVPIRLGQEFEAYSRVLERDIKRIKQSRQHLYEVNMGATAVGTGLNADPEYIK 247 GRTHL DA+P+R+ Q +++ L+ +I ++ + L + G TAVGTG+NA PE+ Sbjct: 179 GRTHLMDAMPVRMSQVLNGWAQQLKANIGHLQDLQPSLQSLAQGGTAVGTGVNAHPEFAA 238 Query: 248 QVVKHLADISGLPLVGADHLVDATQNTDAYTEVSASLKVCMMNMSKIANDLRLMASGPRA 307 + + L+ ++ + L + D VS LK +++ KIANDLR M SGP A Sbjct: 239 RFSQQLSKLTRVEFQPGKDLFALIGSQDTAVAVSGQLKATAVSLMKIANDLRWMNSGPLA 298 Query: 308 GLAEISLPARQPGSSIMPGKVNPVMAELINQIAFQVIGNDNTICLASEAGQLELNVMEPV 367 GL EI L A QPGSSIMPGKVNPV+ E +A QVIGND+ I +A ++G ELNVM P+ Sbjct: 299 GLGEIELQALQPGSSIMPGKVNPVIPEATAMVAAQVIGNDSVITIAGQSGNFELNVMLPI 358 Query: 368 LVFNLLQSISIMNNGFRSFTDNCLKGIEANEKRMKQYVEKSAGVITAVNPHLGYEAAARI 427 + NLL SI ++ N R D + + NE R+K+ + ++ ++TA+NP +GY+ AA I Sbjct: 359 IAQNLLSSIELLANSSRLLADKAIASFKVNEGRIKEALSRNPILVTALNPIIGYQKAAEI 418 Query: 428 AREAIMTGQSVRDLCLQHDVLTEEELDIILNPYEMTKPGI 467 A++A G+ V D+ L+H LT +L+ +LNP ++T G+ Sbjct: 419 AKKAYQQGRPVIDVALEHTDLTRSQLEELLNPEKLTAGGV 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: 527 Number of extensions: 28 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: 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