Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate GFF5380 PS417_27540 argininosuccinate lyase
Query= SwissProt::Q9LAE5 (461 letters) >FitnessBrowser__WCS417:GFF5380 Length = 464 Score = 455 bits (1171), Expect = e-132 Identities = 235/453 (51%), Positives = 305/453 (67%), Gaps = 1/453 (0%) Query: 5 QTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQLVAG 64 Q+W RF + +ARF AS+ FD L +D+ GS AHA MLA G+++ E + ++ G Sbjct: 8 QSWGGRFSEPVDAFVARFTASVTFDQRLYRHDIMGSIAHATMLAKVGVLTDAERDSIIDG 67 Query: 65 LEQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRLYLR 124 L IR E G F VD EDVH +E RLT+ +G GKKLHT RSRNDQV TD RL+LR Sbjct: 68 LTTIRGEIEAGTFDWRVDLEDVHMNIEARLTDRIGVTGKKLHTGRSRNDQVATDIRLWLR 127 Query: 125 DQIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQRDWER 184 D+I I E+ Q LL+ AE+ +T++PG+THLQ AQPV+ HHLLA+F+M RD+ER Sbjct: 128 DEIDLILGEITRLQKGLLEQAERESDTIMPGFTHLQTAQPVTFGHHLLAWFEMLSRDYER 187 Query: 185 LGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFLCAA 244 L D +R N PLG ALAGTT+PIDR YTA+LL FD + NSLDGVSDRDFAIEF AA Sbjct: 188 LVDCRKRANRMPLGSAALAGTTYPIDREYTAQLLGFDAVGGNSLDGVSDRDFAIEFCAAA 247 Query: 245 SLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRVFGH 304 S+ M+HLSR +EE++LW+S +F+F+ L D TGSSIMPQKKNPDVPELVRGK+GRVFG Sbjct: 248 SIAMMHLSRFSEELVLWTSAQFQFIDLPDRFCTGSSIMPQKKNPDVPELVRGKSGRVFGA 307 Query: 305 LQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLAQAVT 364 L +L +MKG PLAYNKD QEDKE LFD+ +T++ SL A ++ ++ + + +A Sbjct: 308 LMGLLTLMKGQPLAYNKDNQEDKEPLFDAADTLRDSLRAFADMI-PAIKPKHAIMREAAL 366 Query: 365 EDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAFAADI 424 FS ATD+ADYL RG+PFR+ + +VG VK + GK L ++ LEE +Q D+ Sbjct: 367 RGFSTATDLADYLVRRGLPFRDCHEIVGHAVKYGVDTGKDLAEMSLEELRQFSDQIEQDV 426 Query: 425 YEAISPRQVVAARNSHGGTGFVQVSKALIAARA 457 + ++ V ARN GGT QV A+ +A Sbjct: 427 FAVLTLEGSVNARNHVGGTAPAQVKAAVARGQA 459 Lambda K H 0.320 0.135 0.384 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: 18 Number of successful extensions: 2 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: 461 Length of database: 464 Length adjustment: 33 Effective length of query: 428 Effective length of database: 431 Effective search space: 184468 Effective search space used: 184468 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)
Align candidate GFF5380 PS417_27540 (argininosuccinate lyase)
to HMM TIGR00838 (argH: argininosuccinate lyase (EC 4.3.2.1))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00838.hmm # target sequence database: /tmp/gapView.1305.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00838 [M=455] Accession: TIGR00838 Description: argH: argininosuccinate lyase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-198 644.7 0.0 5.4e-198 644.5 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF5380 PS417_27540 argininosuccinate ly Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF5380 PS417_27540 argininosuccinate lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 644.5 0.0 5.4e-198 5.4e-198 2 452 .. 10 459 .. 9 462 .. 0.99 Alignments for each domain: == domain 1 score: 644.5 bits; conditional E-value: 5.4e-198 TIGR00838 2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklelev 76 wggR+++ +d va+f+as++fD++l+++Di gsiah+++Lak+g+lt+ e++ +i++L++++ e+++g+++++v lcl|FitnessBrowser__WCS417:GFF5380 10 WGGRFSEPVDAFVARFTASVTFDQRLYRHDIMGSIAHATMLAKVGVLTDAERDSIIDGLTTIRGEIEAGTFDWRV 84 9************************************************************************** PP TIGR00838 77 daeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpg 151 d eD+H+++E++l+d++g gkklhtgrsRnDqvatd+rl+lrd+++ ++ ++ l+k l+e+Ae+e +t+mpg lcl|FitnessBrowser__WCS417:GFF5380 85 DLEDVHMNIEARLTDRIG-VTGKKLHTGRSRNDQVATDIRLWLRDEIDLILGEITRLQKGLLEQAERESDTIMPG 158 ******************.99****************************************************** PP TIGR00838 152 ytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvenslda 226 +tHLq AqP+t++Hhlla++eml+rD+eRl+d kR+n+ PlGs+Alagt+++idre++a+lLgFdav nsld+ lcl|FitnessBrowser__WCS417:GFF5380 159 FTHLQTAQPVTFGHHLLAWFEMLSRDYERLVDCRKRANRMPLGSAALAGTTYPIDREYTAQLLGFDAVGGNSLDG 233 *************************************************************************** PP TIGR00838 227 vsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnl 301 vsdRDf+iE+ +aa+++m+hlsr++Eel+l++s+ f+f++l+d++++gssimPqKKnpDv El+Rgk+grv+G l lcl|FitnessBrowser__WCS417:GFF5380 234 VSDRDFAIEFCAAASIAMMHLSRFSEELVLWTSAQFQFIDLPDRFCTGSSIMPQKKNPDVPELVRGKSGRVFGAL 308 *************************************************************************** PP TIGR00838 302 tglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkG 376 +gllt++K++PlaYnkD qEdke+lfda +t++++l++++ ++ +k ++ ++eaa ++f++atdlAdylvr+G lcl|FitnessBrowser__WCS417:GFF5380 309 MGLLTLMKGQPLAYNKDNQEDKEPLFDAADTLRDSLRAFADMIPAIKPKHAIMREAALRGFSTATDLADYLVRRG 383 *************************************************************************** PP TIGR00838 377 vPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaieeak 451 +PFR+ heivG++v++ +++Gk+l e++leel+++s ++e+dv+ vl+le +v++r+ GGta+++v+ a++ + lcl|FitnessBrowser__WCS417:GFF5380 384 LPFRDCHEIVGHAVKYGVDTGKDLAEMSLEELRQFSDQIEQDVFAVLTLEGSVNARNHVGGTAPAQVKAAVARGQ 458 **********************************************************************98766 PP TIGR00838 452 a 452 a lcl|FitnessBrowser__WCS417:GFF5380 459 A 459 5 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (464 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.04 # Mc/sec: 4.62 // [ok]
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