Align Argininosuccinate lyase; ASAL; EC 4.3.2.1; Arginosuccinase (uncharacterized)
to candidate WP_011993154.1 XAUT_RS25620 argininosuccinate lyase
Query= curated2:A3CTT5 (492 letters) >NCBI__GCF_000017645.1:WP_011993154.1 Length = 505 Score = 208 bits (529), Expect = 4e-58 Identities = 149/466 (31%), Positives = 219/466 (46%), Gaps = 24/466 (5%) Query: 38 LVDMAHLLGLSRQGIIDEAPARALMAALLDLYDHGVPEEAFDERFEDVHAGKEAYLIDRV 97 LV+ AH++ LS +G+I APAR L+ ALLDL+ G + D++ EA + R Sbjct: 48 LVEFAHVITLSERGVIPRAPARELVGALLDLHAGGSTGAVAE--LGDLYTNHEAQVAQRT 105 Query: 98 GEDFGGRLHMGRSRNDEVATCIRIRLKEEIIALLRSLVDLRATLLDVAAGHTGTVMPGFT 157 G L R+R + + T + ++E ++AL SL L L A H VMP +T Sbjct: 106 KAV--GWLGTARARREALTTAYHLLVRERLLALGTSLARLGRALAVTALTHADDVMPDYT 163 Query: 158 HLQHAQPTTLAHYLLAYEQAFSRDTARLREAYARVDVSPLGSAAFASTGFPLDRAYTASL 217 +LQ AQPT+ HY+L + RD RL+ Y R D+ P G + + DRA A Sbjct: 164 YLQAAQPTSFGHYVLGFAAPVMRDLERLQSLYGRADLCPAGCGSMNGSVAFQDRAALAQR 223 Query: 218 LGFSRPAGNSMDAVAARDFAIEVLADASICMTSTSRLCEELVLWSTAFVGFVRLDDAYCS 277 LGFS P + DA+ D AIE +A + RL E+L++++TA G VRL D + Sbjct: 224 LGFSGPLAHGRDAMWQADLAIEAMALSVAASVGLDRLAEDLMIFATAEFGLVRLSDRHSR 283 Query: 278 SSSIMPQKKNPDVAEIMRAKAGSVAGSLAAAITITKGLPMSYNRDLQELTPHLWRGVEAA 337 +S I+PQK+NP +R A + G +AA + + P + + + ++A Sbjct: 284 ASKILPQKRNPYALAFVRGLANRLIG-VAAGVAASGRTPTGQMDNRMQSYGAVPEALDAC 342 Query: 338 RQSIPLLSGMLGSATFDAERMAAEAGRGFSTATELADVLVREYGLPFRTAHRIVGRAVRH 397 ++ L++ ++G+ TFDA R A G A++LA+ L G+ FR+AH +VGR V Sbjct: 343 AKAADLMAEVIGALTFDAARARALLADGACFASDLAERLCLVLGVDFRSAHGLVGRLV-- 400 Query: 398 GSLDLATLEAAAREAADFSVVELGLTREKIDAVL------------DPRHAVAVRNIVGG 445 LE R A S EL D L DP+ + R +GG Sbjct: 401 -----TRLEQEGRTLASLSQSELSDACRAYDETLPAVPDGLLAEAFDPKACLEARRDIGG 455 Query: 446 PAPEAVAAQISEQRNLLARDKAWAEETESALSGAFEHLILEARRFA 491 AP V Q E + T + A L+ EAR FA Sbjct: 456 AAPAQVRRQAREFDDTFRHRAQDLAATTHRHAAALSRLVDEARSFA 501 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: 622 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