Align Aspartate ammonia-lyase; Aspartase; EC 4.3.1.1 (uncharacterized)
to candidate PP_0944 PP_0944 fumarate hydratase (class 2)
Query= curated2:P26899 (475 letters) >FitnessBrowser__Putida:PP_0944 Length = 459 Score = 350 bits (899), Expect = e-101 Identities = 190/460 (41%), Positives = 279/460 (60%), Gaps = 7/460 (1%) Query: 9 RVEKDFLGEKQIEADVYYGIQTLRASENFPITGYKIHEEMINALAIVKKAAALANMDVKR 68 R+E+D +GE Q+ A YG QT RA +NFPI+G ++ + I AL + K AAA AN+++++ Sbjct: 6 RIERDSMGELQVPAQALYGAQTQRAVDNFPISGQRMPAQFIRALLLAKAAAAKANVELEQ 65 Query: 69 LYEGIGQAIVQAADEILEGKWHDQFIVDPIQGGAGTSMNMNANEVIGNRALEIMGHKKGD 128 L G GQAIV+A +++L + F VD Q G+GTS NMNANEVI A ++G Sbjct: 66 LSAGQGQAIVKAVEQLLAEDFIQHFPVDVFQTGSGTSSNMNANEVIATLATHVLGEA--- 122 Query: 129 YIHLSPNTHVNMSQSTNDVFPTAIHIST-LKLLEKLLKTMEDMHSVFKQKAQEFDSVIKM 187 ++ N HVN QS+ND+ PT IH+S L L E+LL + + V + K+ + +K Sbjct: 123 ---VNANDHVNCGQSSNDIIPTTIHVSAALALHEQLLPALAHLVQVIEVKSAQVHQYVKT 179 Query: 188 GRTHLQDAVPIRLGQEFEAYSRVLERDIKRIKQSRQHLYEVNMGATAVGTGLNADPEYIK 247 GRTHL DA+P+R+ Q + ++ + I+ HL + G TAVGTG+NA P++ Sbjct: 180 GRTHLMDAMPVRMSQVLDGWAAQINAAKSHIEGVLPHLQALAQGGTAVGTGINAHPQFAV 239 Query: 248 QVVKHLADISGLPLVGADHLVDATQNTDAYTEVSASLKVCMMNMSKIANDLRLMASGPRA 307 + L+ ++ + +L + D +S LK + + KIANDLR M SGP A Sbjct: 240 GFARQLSGLTKVEFTPGQNLFALIGSQDTAVALSGQLKTTAVALMKIANDLRWMNSGPLA 299 Query: 308 GLAEISLPARQPGSSIMPGKVNPVMAELINQIAFQVIGNDNTICLASEAGQLELNVMEPV 367 GL EI L A QPGSSIMPGKVNPV+ E +A QVIGND TI +A +AG ELNVM PV Sbjct: 300 GLGEIELQALQPGSSIMPGKVNPVIPEATAMVAAQVIGNDATIAVAGQAGNFELNVMLPV 359 Query: 368 LVFNLLQSISIMNNGFRSFTDNCLKGIEANEKRMKQYVEKSAGVITAVNPHLGYEAAARI 427 + NLL+SI +M N R D + + NE ++K+ + ++ ++TA+NP +GY AA I Sbjct: 360 IARNLLESIELMANVSRLLADKAIASFKVNEDKLKEALARNPILVTALNPIIGYLKAAEI 419 Query: 428 AREAIMTGQSVRDLCLQHDVLTEEELDIILNPYEMTKPGI 467 A+ A G+ + D+ L+H L+ ++L+ +L+P ++T GI Sbjct: 420 AKTAYKQGRPIIDVALEHTDLSRDQLEALLDPEKLTAGGI 459 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: 530 Number of extensions: 29 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: 459 Length adjustment: 33 Effective length of query: 442 Effective length of database: 426 Effective search space: 188292 Effective search space used: 188292 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