Align Argininosuccinate lyase; ASAL; EC 4.3.2.1; Arginosuccinase (uncharacterized)
to candidate WP_011993169.1 XAUT_RS25700 argininosuccinate lyase
Query= curated2:Q2J867 (464 letters) >NCBI__GCF_000017645.1:WP_011993169.1 Length = 483 Score = 150 bits (378), Expect = 1e-40 Identities = 139/463 (30%), Positives = 204/463 (44%), Gaps = 48/463 (10%) Query: 5 GGRFAGGPAEALARLSISVQFDWR--LAPYDLLASKSHARVLHRAGLLDADELAAMLAAL 62 G R P+E L + + + + L + L +H L G++ ++AAL Sbjct: 16 GNRLLEAPSERLVASAFAEEVSGQDELFRHLGLVVLAHCITLTEQGVIPPAPARLLVAAL 75 Query: 63 DELSDA----VAQGRFRPTVEDEDVHTALERGLLERLGTLGGKLRAGRSRNDQVATDLRL 118 EL A VA+ F D++T E L R+ G R+R + + T L Sbjct: 76 IELQQAGSGFVAEAGFG------DLYTNRE-AYLTRVTPAVGWFGTSRARREALTTAYHL 128 Query: 119 YLRDSAREVAARLTELSHALVVLAEQHVDTPAPGMTHLQHAQPISFGHQLLAHVQAFVRD 178 LR+ E+ L L A+V +AE HV++ P T+LQ AQP SFG L +RD Sbjct: 129 SLRERLTELGLALVRLGRAIVTVAETHVESVMPDYTYLQAAQPTSFGRYLSGFAWPALRD 188 Query: 179 IDRLRDWDVRASVSALGAGALAGSSLPLDPQGVAAELGFDRA--FANSLDAVSDRDFAAE 236 + RL VR + G G++ GS VA + DRA A++ DA+ D E Sbjct: 189 LQRLEALYVRVDLCPAGCGSINGS--------VAFQ---DRAAPLAHARDAMWQADLTIE 237 Query: 237 FLFVAALIGVHLSRLGEEIVLWTTREFGWVELDDAFATGSSIMPQKKNPDVAELARGKSG 296 + +A V L R+ E+++ + T EFG+V L D S IMPQK+NP V RG + Sbjct: 238 AIGLAVAAVVGLDRIAEDLMSFATAEFGFVRLSDRHGRASKIMPQKRNPFVLAFVRGGAN 297 Query: 297 RLIGDLTGFLATLKGLPLAYDRDLQEDKEPVFDAVDTLLLVLPALTGTVATMRVRRERLV 356 RLIG+ G A+ + + + + A LL+ +T + ER Sbjct: 298 RLIGEQAGVAASGR----------MDSRMLPYVAAQAALLMAEVIT----ELSSDNERAR 343 Query: 357 AAAPDGFALATDVAEYL-VRRGVPFRQAHEAVGQFVSWCVAHDVDLDEVSDDDL------ 409 AA DG A+D+AE L + + FR AH VG+ + + L +++ +L Sbjct: 344 AAIDDGITCASDLAERLCLTLDLDFRTAHGVVGRLIGRLESEGRVLASLTEAELQVACRN 403 Query: 410 -GMINPLLTPDVREVLSVRGALEARSAPGGTAPDRVREQIAAL 451 G PL +R L L AR GG AP V QI L Sbjct: 404 AGAKRPLPDGLLRSALDPACCLRARGDVGGAAPREVVRQIGEL 446 Lambda K H 0.321 0.137 0.400 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: 495 Number of extensions: 26 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: 464 Length of database: 483 Length adjustment: 33 Effective length of query: 431 Effective length of database: 450 Effective search space: 193950 Effective search space used: 193950 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: 51 (24.3 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