Align Argininosuccinate lyase; ASAL; EC 4.3.2.1; Arginosuccinase (uncharacterized)
to candidate WP_011992986.1 XAUT_RS24685 argininosuccinate lyase
Query= curated2:A3CTT5 (492 letters) >NCBI__GCF_000017645.1:WP_011992986.1 Length = 505 Score = 200 bits (508), Expect = 1e-55 Identities = 138/433 (31%), Positives = 206/433 (47%), Gaps = 24/433 (5%) Query: 37 LLVDMAHLLGLSRQGIIDEAPARALMAALLDLYDHGVPEEAFDERFEDVHAGKEAYLIDR 96 +LVD+AH++ L+ + +I PAR L+ ALLDL+D G E + D++ EA + R Sbjct: 47 VLVDLAHVITLAERDVIPRGPARDLVGALLDLHDEGGAEALAE--LGDLYTNHEARIAAR 104 Query: 97 VGEDFGGRLHMGRSRNDEVATCIRIRLKEEIIALLRSLVDLRATLLDVAAGHTGTVMPGF 156 G L R+R + + T + L+E ++ L +L L L A H VMP + Sbjct: 105 TAA--AGWLGTARARREALTTAYHLLLRERLLVLGTALTRLGRRLAAAALAHADQVMPDY 162 Query: 157 THLQHAQPTTLAHYLLAYEQAFSRDTARLREAYARVDVSPLGSAAFASTGFPLDRAYTAS 216 T+LQ AQPT+L HYLL + RD RL Y R D+ P G + + DRA + Sbjct: 163 TYLQAAQPTSLGHYLLGFAWPVLRDLGRLEALYVRTDLCPAGCGSMNGSVAFQDRAALSR 222 Query: 217 LLGFSRPAGNSMDAVAARDFAIEVLADASICMTSTSRLCEELVLWSTAFVGFVRLDDAYC 276 LGFS P + DA+ D AIE +A + RL E+L++++TA G VRL D + Sbjct: 223 RLGFSSPLAHGRDAMWQADLAIEAMALSVTASVGLDRLAEDLMIFATAEFGLVRLADKHS 282 Query: 277 SSSSIMPQKKNPDVAEIMRAKAGSVAGSLAAAITITKGLPMSYNRDLQELTPHLWRGVEA 336 +S I+PQK+NP +R A + G+ A + + P + + + + Sbjct: 283 RASKILPQKRNPYALAFIRGLANRLIGA-QAGVAASARTPTGQMDNRMLAYGAVPEALGS 341 Query: 337 ARQSIPLLSGMLGSATFDAERMAAEAGRGFSTATELADVLVREYGLPFRTAHRIVGRAVR 396 ++ L++ ++G+ +FD R A G A++LA+ L GL FR AH +VGR V Sbjct: 342 CAEATDLMAEIIGALSFDGARAEALLADGACFASDLAERLCLALGLDFRRAHGLVGRLV- 400 Query: 397 HGSLDLATLEAAAREAADFSVVELGLTREKIDAVL------------DPRHAVAVRNIVG 444 LE R + + EL DA L DP+ + R VG Sbjct: 401 ------TRLEGEERALSTLTQDELSAACHAFDAALPPVPDGLLAAAFDPKTCLEARRDVG 454 Query: 445 GPAPEAVAAQISE 457 G AP+ V Q E Sbjct: 455 GAAPQEVRRQARE 467 Lambda K H 0.321 0.133 0.381 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: 611 Number of extensions: 27 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: 492 Length of database: 505 Length adjustment: 34 Effective length of query: 458 Effective length of database: 471 Effective search space: 215718 Effective search space used: 215718 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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