Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate WP_013258686.1 DEBA_RS09390 argininosuccinate lyase
Query= SwissProt::Q9LAE5 (461 letters) >NCBI__GCF_000143965.1:WP_013258686.1 Length = 469 Score = 440 bits (1132), Expect = e-128 Identities = 235/461 (50%), Positives = 304/461 (65%), Gaps = 5/461 (1%) Query: 3 KEQTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQLV 62 + + W RF H + R NASI FD L D+ GS+AHA MLA G+IS+ + + Sbjct: 6 QHKLWGGRFAENTHQMMERINASIDFDKRLYRQDIAGSKAHAAMLARQGVISAADEAAIQ 65 Query: 63 AGLEQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRLY 122 AGL+Q+ E G+ ED+H VE RL +I+G +LHT RSRNDQV TD RL+ Sbjct: 66 AGLDQVLAEIEAGQMAWRQSLEDIHTHVESRLAQIIGAPAGRLHTGRSRNDQVATDLRLW 125 Query: 123 LRDQIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQRDW 182 + + +++ L E+Q L+ +AEKHV++++PGYTHLQRAQPV LAHHLLAY +MA RD Sbjct: 126 VLEAGRELDQALAEYQRALVALAEKHVDSIMPGYTHLQRAQPVVLAHHLLAYVEMAWRDR 185 Query: 183 ERLGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFLC 242 RL D R ISPLG ALAGTTFP+D A+ L F+ ++ANSLD VSDRDFA EF+ Sbjct: 186 GRLADCLGRAAISPLGAAALAGTTFPLDPRSVAEALGFEGVFANSLDAVSDRDFAAEFIF 245 Query: 243 AASLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRVF 302 L+ VHLSRLAEE+I+WS+ EF FV L D+ +TGSSIMPQKKNPD EL+RGKTGRV Sbjct: 246 VLGLVQVHLSRLAEELIIWSTSEFGFVTLSDAFSTGSSIMPQKKNPDAAELIRGKTGRVL 305 Query: 303 GHLQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLAQA 362 G L +L ++KGLPLAYNKD+QEDKE +FD+ +TV L M+ +L + L R RLAQA Sbjct: 306 GDLVGILTVLKGLPLAYNKDMQEDKEPVFDAHDTVMDCLRVMSPMLAD-LTVRADRLAQA 364 Query: 363 VTEDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAFAA 422 V F NAT++ADYLA RG PFR A+ G+ V+ + A + L+DL L+E + A Sbjct: 365 VGGGFLNATELADYLAERGAPFRLAHEATGRAVRLAEAGDRGLEDLTLDELRDCCGGLAV 424 Query: 423 DI----YEAISPRQVVAARNSHGGTGFVQVSKALIAARAQI 459 DI Y+A+ P + V R S GGT V +AL AR ++ Sbjct: 425 DIDQTVYQALKPERAVDRRTSPGGTARANVERALKEARKRL 465 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: 538 Number of extensions: 22 Number of successful extensions: 3 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: 469 Length adjustment: 33 Effective length of query: 428 Effective length of database: 436 Effective search space: 186608 Effective search space used: 186608 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_013258686.1 DEBA_RS09390 (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.20016.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-186 605.3 0.0 4.8e-186 605.1 0.0 1.0 1 lcl|NCBI__GCF_000143965.1:WP_013258686.1 DEBA_RS09390 argininosuccinate l Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000143965.1:WP_013258686.1 DEBA_RS09390 argininosuccinate lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 605.1 0.0 4.8e-186 4.8e-186 1 454 [. 9 465 .. 9 466 .. 0.98 Alignments for each domain: == domain 1 score: 605.1 bits; conditional E-value: 4.8e-186 TIGR00838 1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevke 69 lwggR+++++++ +++ nas++fDk+l+++Di gs+ah+++La++g++++ +++ ++++L+++ e+++ lcl|NCBI__GCF_000143965.1:WP_013258686.1 9 LWGGRFAENTHQMMERINASIDFDKRLYRQDIAGSKAHAAMLARQGVISAADEAAIQAGLDQVLAEIEA 77 7******************************************************************** PP TIGR00838 70 gklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalv 138 g++ ++++ eDiH+ vE++l + +g +g +lhtgrsRnDqvatdlrl++ ++ +el +al + ++alv lcl|NCBI__GCF_000143965.1:WP_013258686.1 78 GQMAWRQSLEDIHTHVESRLAQIIGAPAG-RLHTGRSRNDQVATDLRLWVLEAGRELDQALAEYQRALV 145 *************************7777.*************************************** PP TIGR00838 139 ekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidr 207 +Aek+v+ +mpgytHLqrAqP+ laHhllay+em rD Rl d l R++ sPlG++Alagt+f++d+ lcl|NCBI__GCF_000143965.1:WP_013258686.1 146 ALAEKHVDSIMPGYTHLQRAQPVVLAHHLLAYVEMAWRDRGRLADCLGRAAISPLGAAALAGTTFPLDP 214 ********************************************************************* PP TIGR00838 208 ellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgss 276 +++ae LgF+ v +nsldavsdRDf++E+++++ l+ vhlsrlaEeli++s++Efgfv+lsd++s+gss lcl|NCBI__GCF_000143965.1:WP_013258686.1 215 RSVAEALGFEGVFANSLDAVSDRDFAAEFIFVLGLVQVHLSRLAEELIIWSTSEFGFVTLSDAFSTGSS 283 ********************************************************************* PP TIGR00838 277 imPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllk 345 imPqKKnpD+aEliRgktgrv G+l+g+lt+lK+lPlaYnkD+qEdke++fda +tv ++l+v+ +l+ lcl|NCBI__GCF_000143965.1:WP_013258686.1 284 IMPQKKNPDAAELIRGKTGRVLGDLVGILTVLKGLPLAYNKDMQEDKEPVFDAHDTVMDCLRVMSPMLA 352 ********************************************************************* PP TIGR00838 346 elkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqk.... 410 +l+v+ +rl++a+ +f +at+lAdyl+++G PFR ahe +G++v+ a++ +le+ltl+el+ lcl|NCBI__GCF_000143965.1:WP_013258686.1 353 DLTVRADRLAQAVGGGFLNATELADYLAERGAPFRLAHEATGRAVRLAEAGDRGLEDLTLDELRDccgg 421 **********************************************9999888*********9973322 PP TIGR00838 411 lsekleedvlevldleeavekrdakGGtakeevekaieeakael 454 l +++ v+++l++e+av++r++ GGta ++ve+a++ea+++l lcl|NCBI__GCF_000143965.1:WP_013258686.1 422 LAVDIDQTVYQALKPERAVDRRTSPGGTARANVERALKEARKRL 465 56788888********************************9886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (469 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: 00:00:00.02 # Mc/sec: 7.78 // [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