Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate WP_084703910.1 BS73_RS08890 argininosuccinate lyase
Query= BRENDA::P9WPY7 (470 letters) >NCBI__GCF_000744815.1:WP_084703910.1 Length = 494 Score = 607 bits (1564), Expect = e-178 Identities = 307/462 (66%), Positives = 368/462 (79%), Gaps = 1/462 (0%) Query: 8 LWGGRFAGGPSDALAALSKSTHFDWVLAPYDLTASRAHTMVLFRAGLLTEEQRDGLLAGL 67 LWGGRFA GPS+ALAALS S HFDW LAPYD+ SRAH VL +AGLLT+E+ + +LAGL Sbjct: 31 LWGGRFADGPSEALAALSASVHFDWRLAPYDIAGSRAHARVLHKAGLLTDEELERMLAGL 90 Query: 68 DSLAQDVADGSFGPLVTDEDVHAALERGLIDRVGPDLGGRLRAGRSRNDQVAALFRMWLR 127 D L DV G F V DEDVH ALERGL++R+GP+LGG+LRAGRSRNDQ+A L RM+LR Sbjct: 91 DRLLADVESGDFVGTVADEDVHTALERGLLERLGPELGGKLRAGRSRNDQIATLGRMYLR 150 Query: 128 DAVRRVATGVLDVVGALAEQAAAHPSAIMPGKTHLQSAQPILLAHHLLAHAHPLLRDLDR 187 D R V +L++ AL A AHP A MPG+THLQ AQP+L AHH+LAH L RD +R Sbjct: 151 DHGRTVGRLLLELQEALVGLAEAHPKAAMPGRTHLQHAQPVLFAHHMLAHVAALGRDAER 210 Query: 188 IVDFDKRAAVSPYGSGALAGSSLGLDPDAIAADLGFS-AAADNSVDATAARDFAAEAAFV 246 + +D+R AVSPYGSGALAGSSLGLDP+A+AA+LGF ++ NS+D TAARD+ AE AFV Sbjct: 211 LRQWDERTAVSPYGSGALAGSSLGLDPEAVAAELGFERGSSGNSIDGTAARDYVAEFAFV 270 Query: 247 FAMIAVDLSRLAEDIIVWSSTEFGYVTLHDSWSTGSSIMPQKKNPDIAELARGKSGRLIG 306 AMI +DLSR+AE+II+W++ EFG++TLHD++STGSSIMPQKKNPDIAELARGKSGRLIG Sbjct: 271 TAMIGIDLSRIAEEIILWNTKEFGFITLHDAFSTGSSIMPQKKNPDIAELARGKSGRLIG 330 Query: 307 NLAGLLATLKAQPLAYNRDLQEDKEPVFDSVAQLELLLPAMAGLVASLTFNVQRMAELAP 366 NL GLLATLKA PLAYNRDLQEDKEPVFDSV LE+LLPA G++A+LT + +RMAELAP Sbjct: 331 NLTGLLATLKALPLAYNRDLQEDKEPVFDSVDTLEVLLPAFIGMMATLTVHEERMAELAP 390 Query: 367 AGYTLATDLAEWLVRQGVPFRSAHEAAGAAVRAAEQRGVGLQELTDDELAAISPELTPQV 426 AG++LATD+AEWLVRQG PFR AHE AGA V+ E RG+ L +LTD + A ISP LTP+V Sbjct: 391 AGFSLATDIAEWLVRQGTPFRVAHEVAGACVKFCEPRGLELSDLTDAQFAEISPLLTPEV 450 Query: 427 REVLTIEGSVSARDCRGGTAPGRVAEQLNAIGEAAERLRRQL 468 R VLT+EG++++RD RGGTAP VA QL + R R L Sbjct: 451 RSVLTVEGAIASRDGRGGTAPAAVARQLTEVAADLARQREWL 492 Lambda K H 0.318 0.133 0.382 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: 677 Number of extensions: 30 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: 470 Length of database: 494 Length adjustment: 34 Effective length of query: 436 Effective length of database: 460 Effective search space: 200560 Effective search space used: 200560 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
Align candidate WP_084703910.1 BS73_RS08890 (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.737764.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.7e-182 590.9 0.0 1.1e-181 590.7 0.0 1.0 1 NCBI__GCF_000744815.1:WP_084703910.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_084703910.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 590.7 0.0 1.1e-181 1.1e-181 1 454 [. 31 485 .. 31 486 .. 0.99 Alignments for each domain: == domain 1 score: 590.7 bits; conditional E-value: 1.1e-181 TIGR00838 1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegkle 73 lwggR+++++++a+a+++as++fD++la +Di gs ah+++L+kag+lt+ee +++ ++L++l +v++g++ NCBI__GCF_000744815.1:WP_084703910.1 31 LWGGRFADGPSEALAALSASVHFDWRLAPYDIAGSRAHARVLHKAGLLTDEELERMLAGLDRLLADVESGDFV 103 7************************************************************************ PP TIGR00838 74 levdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekeve 146 +v +eD+H+a+Er l +++g ++g+kl++grsRnDq+at r+ylrd+ +++ + l++l++alv +Ae++ + NCBI__GCF_000744815.1:WP_084703910.1 104 GTVADEDVHTALERGLLERLGPELGGKLRAGRSRNDQIATLGRMYLRDHGRTVGRLLLELQEALVGLAEAHPK 176 ************************************************************************* PP TIGR00838 147 tlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFda. 218 + mpg tHLq+AqP+ +aHh+la++ +l rD eRl + +R+++sP+GsgAlag+s+++d+e++a+ LgF++ NCBI__GCF_000744815.1:WP_084703910.1 177 AAMPGRTHLQHAQPVLFAHHMLAHVAALGRDAERLRQWDERTAVSPYGSGALAGSSLGLDPEAVAAELGFERg 249 **********************************************************************973 PP TIGR00838 219 vvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliR 291 ns+d++++RD+++E+ +++a++ ++lsr+aEe+il++++Efgf++l+d++s+gssimPqKKnpD+aEl+R NCBI__GCF_000744815.1:WP_084703910.1 250 SSGNSIDGTAARDYVAEFAFVTAMIGIDLSRIAEEIILWNTKEFGFITLHDAFSTGSSIMPQKKNPDIAELAR 322 678********************************************************************** PP TIGR00838 292 gktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfal 364 gk+gr+iGnltgll++lKalPlaYn+DlqEdke++fd+++t+e ll ++ g++++l+v++er++e+a ++f+l NCBI__GCF_000744815.1:WP_084703910.1 323 GKSGRLIGNLTGLLATLKALPLAYNRDLQEDKEPVFDSVDTLEVLLPAFIGMMATLTVHEERMAELAPAGFSL 395 ************************************************************************* PP TIGR00838 365 atdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGG 437 atd+A++lvr+G PFR ahe++G++v+ ++ +G++l++lt ++++++s+ l+++v++vl++e a++ rd +GG NCBI__GCF_000744815.1:WP_084703910.1 396 ATDIAEWLVRQGTPFRVAHEVAGACVKFCEPRGLELSDLTDAQFAEISPLLTPEVRSVLTVEGAIASRDGRGG 468 ************************************************************************* PP TIGR00838 438 takeevekaieeakael 454 ta+++v++++ e+ a+l NCBI__GCF_000744815.1:WP_084703910.1 469 TAPAAVARQLTEVAADL 485 **********9998876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (494 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 17.49 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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