Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate WP_013682981.1 ARCVE_RS01335 argininosuccinate lyase
Query= SwissProt::Q9LAE5 (461 letters) >NCBI__GCF_000194625.1:WP_013682981.1 Length = 486 Score = 319 bits (818), Expect = 1e-91 Identities = 182/429 (42%), Positives = 260/429 (60%), Gaps = 12/429 (2%) Query: 24 ASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQLVAGLEQIRQEHRQGKFHPGVDA 83 +S+ D + YD+ AH L G ISSE+ ++ + ++R E G G Sbjct: 21 SSLEHDRNIFFYDILVDLAHVLTLLKAGHISSEDAIPILKAILEVRDE---GMPEGG--- 74 Query: 84 EDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRLYLRDQIQQIKSELREFQGVLLD 143 EDVH A+E R+ E G G K+HTARSRND++ T RL+ RD + + L + VLL+ Sbjct: 75 EDVHEAIEARIIEKAGSAGMKMHTARSRNDEIATCLRLFARDSLLHLAYSLLNLREVLLN 134 Query: 144 IAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQRDWERLGDVSRRVNISPLGCGALA 203 AE++++ ++PG+THLQ AQP L+HHL+AY M RD++R D +R+N+ PLG A A Sbjct: 135 RAEEYIDAVMPGFTHLQYAQPTKLSHHLIAYHDMITRDFQRCMDAFKRINLCPLGSAAFA 194 Query: 204 GTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFLCAASLIMVHLSRLAEEVILWSS 263 T F +DRHYTAKLL FD I NS D + RDF IE + ++ +M+ LSR+AEE+ILW+S Sbjct: 195 STPFQLDRHYTAKLLGFDGIVENSEDATASRDFLIESIFVSTSVMLTLSRIAEEIILWAS 254 Query: 264 EEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRVFGHLQAMLVIMKGLPLAYNKDL 323 EF FV L D A+ SSIMPQKKNPDV E+VR K G++ G+L A + I K +PL+YN+D Sbjct: 255 -EFGFVELPDEYASSSSIMPQKKNPDVAEIVRAKAGKLTGNLMAAMAIYKAMPLSYNRDF 313 Query: 324 QEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLAQAVTEDFSNATDVADYLAARGVP 383 QE L+DS+ V S + M +L E ++FRT + + FS AT +AD L GVP Sbjct: 314 QEMNPLLYDSLQCVNLSCDVMAGML-EKVKFRTDVMEEKAGRGFSVATHIADELVKLGVP 372 Query: 384 FREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAFAADIYEAISPRQVVAARNSHGGT 443 FR+A+ +VG+ + + + L K +E E L P + + ++VV AR + GGT Sbjct: 373 FRKAHRIVGR-LSLNPSYENLKKIMEEE---GLEPMDEENFKRCMDVKEVVEARKNIGGT 428 Query: 444 GFVQVSKAL 452 ++ + L Sbjct: 429 SKEEIRQML 437 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: 519 Number of extensions: 28 Number of successful extensions: 5 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: 486 Length adjustment: 33 Effective length of query: 428 Effective length of database: 453 Effective search space: 193884 Effective search space used: 193884 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 WP_013682981.1 ARCVE_RS01335 (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.19084.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-168 547.0 0.4 2.4e-168 546.7 0.4 1.0 1 lcl|NCBI__GCF_000194625.1:WP_013682981.1 ARCVE_RS01335 argininosuccinate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000194625.1:WP_013682981.1 ARCVE_RS01335 argininosuccinate lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 546.7 0.4 2.4e-168 2.4e-168 3 452 .. 5 442 .. 3 445 .. 0.97 Alignments for each domain: == domain 1 score: 546.7 bits; conditional E-value: 2.4e-168 TIGR00838 3 ggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegk 71 ++Rlk+e+d + ++++sl++D +++ +Di +++ah+ +L kag +++e+a + +a+ e+++e++ + lcl|NCBI__GCF_000194625.1:WP_013682981.1 5 RSRLKGEMDRLALTLTSSLEHDRNIFFYDILVDLAHVLTLLKAGHISSEDAIPILKAILEVRDEGMPE- 72 68************************************************************999885. PP TIGR00838 72 lelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvek 140 eD+H+a+E+++i+k g +g k+ht+rsRnD++at+lrl++rd++ +la +l++l+++l+++ lcl|NCBI__GCF_000194625.1:WP_013682981.1 73 -----GGEDVHEAIEARIIEKAG-SAGMKMHTARSRNDEIATCLRLFARDSLLHLAYSLLNLREVLLNR 135 .....89****************.9******************************************** PP TIGR00838 141 AekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrel 209 Ae+ ++++mpg+tHLq+AqP++l+Hhl+ay++m++rD++R +da+kR+n +PlGs+A+a+t f++dr++ lcl|NCBI__GCF_000194625.1:WP_013682981.1 136 AEEYIDAVMPGFTHLQYAQPTKLSHHLIAYHDMITRDFQRCMDAFKRINLCPLGSAAFASTPFQLDRHY 204 ********************************************************************* PP TIGR00838 210 laelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssim 278 +a+lLgFd +vens da+++RDf+iE++++++ +m+ lsr+aEe+il++s Efgfvel+de++s+ssim lcl|NCBI__GCF_000194625.1:WP_013682981.1 205 TAKLLGFDGIVENSEDATASRDFLIESIFVSTSVMLTLSRIAEEIILWAS-EFGFVELPDEYASSSSIM 272 *************************************************9.****************** PP TIGR00838 279 PqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkel 347 PqKKnpDvaE++R+k+g+++Gnl+++++i+Ka+Pl+Yn+D+qE+++ l+d+l+ v+ + +v++g+l+++ lcl|NCBI__GCF_000194625.1:WP_013682981.1 273 PQKKNPDVAEIVRAKAGKLTGNLMAAMAIYKAMPLSYNRDFQEMNPLLYDSLQCVNLSCDVMAGMLEKV 341 ********************************************************************* PP TIGR00838 348 kvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsekle 416 k++++ +ee+a ++f+ at +Ad lv+ GvPFR+ah+ivG++ + + +l+++ ee + + e lcl|NCBI__GCF_000194625.1:WP_013682981.1 342 KFRTDVMEEKAGRGFSVATHIADELVKLGVPFRKAHRIVGRLSLNPSYE--NLKKIMEEEGLE--PMDE 406 ******************************************9887776..899999998876..5555 PP TIGR00838 417 edvlevldleeavekrdakGGtakeevekaieeaka 452 e+ ++ +d++e+ve+r+++GGt+kee+++++e + + lcl|NCBI__GCF_000194625.1:WP_013682981.1 407 ENFKRCMDVKEVVEARKNIGGTSKEEIRQMLEDRLS 442 56****************************998765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (486 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 9.69 // [ok]
This GapMind analysis is from Apr 10 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