Align Argininosuccinate lyase; ASAL; EC 4.3.2.1; Arginosuccinase (uncharacterized)
to candidate WP_244403893.1 PYRFU_RS03710 lyase family protein
Query= curated2:A3MT36 (429 letters) >NCBI__GCF_000223395.1:WP_244403893.1 Length = 457 Score = 249 bits (635), Expect = 2e-70 Identities = 167/411 (40%), Positives = 225/411 (54%), Gaps = 13/411 (3%) Query: 14 LVRRYTSSMADDVEIAEEVVKILKTHVAHLAEVGVIPREAAERIAKALDEV----DYDAL 69 LV+ Y SS D IA +VVK+ HVA LAE ++ + A ++A AL + + Sbjct: 14 LVQDYISSTPHDHMIAHDVVKVALIHVAILAEHNLLDKSNACKLANALQGLLKKPEQLLE 73 Query: 70 AKGGFEDIHEAVEKWVIDRVGEEAGGWLGLGRSRNDHVAAAIRLAALRKLAELKRGLAAL 129 A G+EDIHEA+E + D+ G EA LGRSRNDHVAAA+RL R L ++ L Sbjct: 74 AMKGYEDIHEALEAVLEDKAGREAARSFPLGRSRNDHVAAALRLWTARMLTQIHCEGVEL 133 Query: 130 RCALAKRALQYADCAMPSFTHFQPAQAITFGHYLLSIDELVEEFSRALAGVEPLLKRSPL 189 + K+A ++ D P THFQPAQ T GH++ S E + + + V + +SPL Sbjct: 134 AKTILKKAEEWLDTLFPIHTHFQPAQVGTAGHWIHSYLEPILDALSLIETVFNIAWKSPL 193 Query: 190 GAGPAGGVKTPIDRRRLAKALGFEDVVGNALYASGSRFFASAAASIVVSFLVELSRYVDD 249 G+GP G PIDRRR + V N LYA+GSR FA+AA + V ++ELSR D Sbjct: 194 GSGPGAGTTLPIDRRRYP-----QPPVLNTLYATGSRLFANAAIAAVAVLMIELSRLAAD 248 Query: 250 FIRWNSPAIGYVKAPDSHVSTSSIMPHKRNLVTLEVLRARISEAVGHLTALYAVQAKIGA 309 + + P+I + P+ HVSTSS MPHKRN V+ E+ RAR + G L A V + Sbjct: 249 VVLLSHPSIRVLVPPEHHVSTSSAMPHKRNPVSAEIARARAARVAGLLAAALGVNHGLPH 308 Query: 310 GYSLDLQEATRHLWAILKIAGEGVEVLRDFVEGLEFNCEKARLDAE-TYYATSSDTAEAI 368 GY+LDLQE L+ L E + V RD VEGLE + R E TS + AE + Sbjct: 309 GYNLDLQEENPVLYQALTETLETLRVFRDLVEGLEVDGNAVRRMIEGGAVLTSLEEAERL 368 Query: 369 AL-SGVPFRRAYFQLAEEIKR--GSAKLLSPEEAVKRPTEGSANPEEVRRA 416 A+ SG PFR AY +A+ ++R GS K L P+E K A E ++ A Sbjct: 369 AVNSGTPFRDAYMMVADMVRRSEGSLKPLEPQELYKLRVSLGAAGEGLQEA 419 Lambda K H 0.320 0.134 0.388 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: 430 Number of extensions: 15 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: 429 Length of database: 457 Length adjustment: 32 Effective length of query: 397 Effective length of database: 425 Effective search space: 168725 Effective search space used: 168725 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 (21.8 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