Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate 8499269 DvMF_0048 argininosuccinate lyase (RefSeq)
Query= SwissProt::Q9LAE5 (461 letters) >FitnessBrowser__Miya:8499269 Length = 460 Score = 422 bits (1085), Expect = e-122 Identities = 220/452 (48%), Positives = 289/452 (63%), Gaps = 1/452 (0%) Query: 1 MTKEQTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQ 60 M +++ W RF A + + S+ FD L D+ GS+AHA+MLA G+++++E + Sbjct: 1 MAEKKMWGGRFRQATAALVEEYTQSVSFDRALYAQDIAGSKAHARMLAKQGVLTADEAAR 60 Query: 61 LVAGLEQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTR 120 +V GL+ + E G F + EDVH +E RLTE+VGDVGKKLHT RSRNDQV D R Sbjct: 61 IVEGLDMVLAEIEGGTFVWRRELEDVHMNIESRLTELVGDVGKKLHTGRSRNDQVALDFR 120 Query: 121 LYLRDQIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQR 180 L++ D+I+ + R+ VL + A +H TL+PG TH+Q AQPVSL HHLLAY M +R Sbjct: 121 LFVSDRIRAWRGLARDLVAVLAERAGEHANTLLPGCTHMQPAQPVSLGHHLLAYAWMLRR 180 Query: 181 DWERLGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEF 240 D ERL D RR + PLG ALAGTT+P+D Y A+ LD + NS+D VSDRDF +E Sbjct: 181 DAERLADCDRRTRVCPLGAAALAGTTYPLDPAYVAEQLDMYGTFRNSMDAVSDRDFVLES 240 Query: 241 LCAASLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGR 300 L + IM HLSRL EE+I+W++ F FV L D+ ATGSSIMPQKKNPDV E++RGKTGR Sbjct: 241 LFCGATIMAHLSRLCEEIIIWANPAFGFVRLPDAYATGSSIMPQKKNPDVAEIMRGKTGR 300 Query: 301 VFGHLQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLA 360 V+G L AML +KGLP+ YN+D+QEDKE D TV ASLE M +LRE L F R+ Sbjct: 301 VYGALTAMLTTVKGLPMTYNRDMQEDKEPFLDCDRTVSASLEIMAGMLRE-LGFNEGRMR 359 Query: 361 QAVTEDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAF 420 A+ F NAT++ADYL +G+PFREA++L G V + L++L L + Q + Sbjct: 360 AALRAGFLNATELADYLVGKGIPFREAHHLTGAAVALAEERAITLEELPLADLQAICDRI 419 Query: 421 AADIYEAISPRQVVAARNSHGGTGFVQVSKAL 452 D+Y + P VA R GGTG V+ L Sbjct: 420 GDDVYAVLDPAAAVARREMPGGTGPASVAAQL 451 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: 526 Number of extensions: 14 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: 460 Length adjustment: 33 Effective length of query: 428 Effective length of database: 427 Effective search space: 182756 Effective search space used: 182756 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 8499269 DvMF_0048 (argininosuccinate lyase (RefSeq))
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.3633.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-183 595.3 0.0 4.9e-183 595.2 0.0 1.0 1 lcl|FitnessBrowser__Miya:8499269 DvMF_0048 argininosuccinate lyas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8499269 DvMF_0048 argininosuccinate lyase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 595.2 0.0 4.9e-183 4.9e-183 1 450 [. 6 454 .. 6 459 .. 0.99 Alignments for each domain: == domain 1 score: 595.2 bits; conditional E-value: 4.9e-183 TIGR00838 1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklelevd 77 +wggR+++++ v+e+++s+sfD l+++Di gs+ah+++Lak+g+lt++ea++++e+L+ + e++ g++ ++ + lcl|FitnessBrowser__Miya:8499269 6 MWGGRFRQATAALVEEYTQSVSFDRALYAQDIAGSKAHARMLAKQGVLTADEAARIVEGLDMVLAEIEGGTFVWRRE 82 6**************************************************************************** PP TIGR00838 78 aeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpgytH 154 eD+H+++E++l++ vg dvgkklhtgrsRnDqva d+rl++ d+++ + +dl+++l+e+A ++ +tl+pg tH lcl|FitnessBrowser__Miya:8499269 83 LEDVHMNIESRLTELVG-DVGKKLHTGRSRNDQVALDFRLFVSDRIRAWRGLARDLVAVLAERAGEHANTLLPGCTH 158 *****************.*********************************************************** PP TIGR00838 155 LqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvensldavsdRD 231 +q AqP++l+Hhllaya+ml+rD eRl d +R+ ++PlG++Alagt++++d+ ++ae+L +ns+davsdRD lcl|FitnessBrowser__Miya:8499269 159 MQPAQPVSLGHHLLAYAWMLRRDAERLADCDRRTRVCPLGAAALAGTTYPLDPAYVAEQLDMYGTFRNSMDAVSDRD 235 ***************************************************************************** PP TIGR00838 232 fiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnltglltil 308 f++E+l+ a +m+hlsrl+Ee+i+++ fgfv l+d++++gssimPqKKnpDvaE++Rgktgrv+G lt++lt++ lcl|FitnessBrowser__Miya:8499269 236 FVLESLFCGATIMAHLSRLCEEIIIWANPAFGFVRLPDAYATGSSIMPQKKNPDVAEIMRGKTGRVYGALTAMLTTV 312 ***************************************************************************** PP TIGR00838 309 KalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkGvPFReahei 385 K+lP++Yn+D+qEdke++ d+ +tv+ +le+++g+l+el +n+ r++ a +++f +at+lAdylv kG+PFReah++ lcl|FitnessBrowser__Miya:8499269 313 KGLPMTYNRDMQEDKEPFLDCDRTVSASLEIMAGMLRELGFNEGRMRAALRAGFLNATELADYLVGKGIPFREAHHL 389 ***************************************************************************** PP TIGR00838 386 vGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaieea 450 +G++va a+e+ ++leel+l+ lq++ ++ +dv+ vld+ av++r++ GGt++++v+ +++e+ lcl|FitnessBrowser__Miya:8499269 390 TGAAVALAEERAITLEELPLADLQAICDRIGDDVYAVLDPAAAVARREMPGGTGPASVAAQLAEL 454 ***********************************************************999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (460 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 8.55 // [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