Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate WP_027722612.1 H589_RS0114010 argininosuccinate lyase
Query= BRENDA::Q8DVX5 (460 letters) >NCBI__GCF_000425265.1:WP_027722612.1 Length = 459 Score = 441 bits (1135), Expect = e-128 Identities = 222/453 (49%), Positives = 305/453 (67%) Query: 5 NHKLWGGRFEAGLAQWVEEFGASISFDQKLAEFDLKGSIAHVTMLGEKGIISQEDAATIK 64 ++KLWGGRF A VE++ S+S+D+ L D+ GS AH ML E+G+++ E+A T+ Sbjct: 3 DNKLWGGRFAQKTAASVEDYTESVSYDRNLYREDIAGSQAHAKMLAEQGVLTVEEAETLV 62 Query: 65 AGLEDLLEEYKAGQLKFDVSNEDIHMNMESLLTAKIGPVAGKLHTARSRNDQVATDMHLY 124 GL+ + EE ++G+ ++ ED+HMN+ES LT +G V GKLHT RSRNDQVAT L Sbjct: 63 KGLDQVFEEIESGKFEWKKEMEDLHMNIESRLTEIVGSVGGKLHTGRSRNDQVATTFRLN 122 Query: 125 LKAKLDEVIEKLANLRTVLVDLADKHVHTIMPGYTHLQHAQPISFGHHLMAYYNMFTRDS 184 + L+ L L V A+ H ++PGYTHLQ AQP+S HH++AY MF RD Sbjct: 123 VVHSLEAWKVALEKLIAVFTTKAEAHTDVLLPGYTHLQPAQPVSLAHHMLAYAWMFKRDH 182 Query: 185 ERFIFNVKHTDLSPLGAAALAGTTFPIDREMTAQLMGFAEPYSNSLDAVSDRDFILEFLS 244 R +K ++ PLGAAALAGTT+P+ ++AQ +G + + NSLDAVSDRDF++E + Sbjct: 183 SRVCDCLKRANVCPLGAAALAGTTYPLKPSVSAQHLGMEDTFRNSLDAVSDRDFVMEAMF 242 Query: 245 NASILMMHMSRMCEEVISWCSHEYQFVTLSDTFSTGSSIMPQKKNPDMAELIRGKSGRVY 304 S++M H+SR+CEE+I W + + F+ L D FSTGSSIMPQKKNPD+ EL+RGK+GRVY Sbjct: 243 AGSLIMTHLSRICEELIIWANPCFGFIKLPDAFSTGSSIMPQKKNPDVCELMRGKTGRVY 302 Query: 305 ANLFGLLTVMKALPLAYNKDLQEDKEGMFDTAETITVALDILAGMLSSMIVNDKHMAEST 364 +LF L+T+ K LPLAYN+D+QEDKE FD +T+ ++ I+A M+ +M N ++M + Sbjct: 303 GDLFSLMTICKGLPLAYNRDMQEDKEPFFDVDKTVHASVSIMADMMEAMGFNPQNMKAAL 362 Query: 365 QKDFSNATELADYLASKGMPFRQAHEIVGKLILECSKNGHYLQDVPLERYQTISDLIEED 424 +K F NATELADYL KG+PFR+AH I G + K L+D+ +E +T SD I+ D Sbjct: 363 KKGFLNATELADYLVGKGIPFREAHHITGSAVAYAEKASKGLEDLTIEELKTFSDKIDGD 422 Query: 425 VYETLKSHTAVERRHSLGGTGFEQVKWQIAEAK 457 V+E L AV+RR S GGTG E VK QI+E K Sbjct: 423 VFEILSYEAAVKRRVSPGGTGPESVKAQISELK 455 Lambda K H 0.318 0.132 0.378 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: 576 Number of extensions: 28 Number of successful extensions: 1 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: 460 Length of database: 459 Length adjustment: 33 Effective length of query: 427 Effective length of database: 426 Effective search space: 181902 Effective search space used: 181902 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: 51 (24.3 bits)
Align candidate WP_027722612.1 H589_RS0114010 (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.29965.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-189 617.1 0.0 1.3e-189 616.9 0.0 1.0 1 lcl|NCBI__GCF_000425265.1:WP_027722612.1 H589_RS0114010 argininosuccinate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000425265.1:WP_027722612.1 H589_RS0114010 argininosuccinate lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 616.9 0.0 1.3e-189 1.3e-189 1 452 [. 6 456 .. 6 459 .] 0.99 Alignments for each domain: == domain 1 score: 616.9 bits; conditional E-value: 1.3e-189 TIGR00838 1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevke 69 lwggR+++++ +v+++++s+s+D +l+++Di gs ah+k+La++g+lt eea+ l+++L+++ ee+++ lcl|NCBI__GCF_000425265.1:WP_027722612.1 6 LWGGRFAQKTAASVEDYTESVSYDRNLYREDIAGSQAHAKMLAEQGVLTVEEAETLVKGLDQVFEEIES 74 7******************************************************************** PP TIGR00838 70 gklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalv 138 gk+e+++++eD+H+++E++l++ vg vg+klhtgrsRnDqvat +rl + ++++ + al++l++++ lcl|NCBI__GCF_000425265.1:WP_027722612.1 75 GKFEWKKEMEDLHMNIESRLTEIVG-SVGGKLHTGRSRNDQVATTFRLNVVHSLEAWKVALEKLIAVFT 142 *************************.******************************************* PP TIGR00838 139 ekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidr 207 kAe+++++l+pgytHLq AqP++laHh+laya+m++rD +R+ d lkR+n++PlG++Alagt++++ + lcl|NCBI__GCF_000425265.1:WP_027722612.1 143 TKAEAHTDVLLPGYTHLQPAQPVSLAHHMLAYAWMFKRDHSRVCDCLKRANVCPLGAAALAGTTYPLKP 211 ********************************************************************* PP TIGR00838 208 ellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgss 276 +++a+ Lg ++ +nsldavsdRDf++E+++a +l+m+hlsr++Eeli+++ fgf++l+d++s+gss lcl|NCBI__GCF_000425265.1:WP_027722612.1 212 SVSAQHLGMEDTFRNSLDAVSDRDFVMEAMFAGSLIMTHLSRICEELIIWANPCFGFIKLPDAFSTGSS 280 ********************************************************************* PP TIGR00838 277 imPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllk 345 imPqKKnpDv+El+Rgktgrv+G+l +l+ti K+lPlaYn+D+qEdke++fd ktv+ ++++++ +++ lcl|NCBI__GCF_000425265.1:WP_027722612.1 281 IMPQKKNPDVCELMRGKTGRVYGDLFSLMTICKGLPLAYNRDMQEDKEPFFDVDKTVHASVSIMADMME 349 ********************************************************************* PP TIGR00838 346 elkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsek 414 + +n ++++ a kk+f +at+lAdylv kG+PFReah+i+G++va+a+++ k+le+lt+eel+ +s k lcl|NCBI__GCF_000425265.1:WP_027722612.1 350 AMGFNPQNMKAALKKGFLNATELADYLVGKGIPFREAHHITGSAVAYAEKASKGLEDLTIEELKTFSDK 418 ********************************************************************* PP TIGR00838 415 leedvlevldleeavekrdakGGtakeevekaieeaka 452 ++ dv+e+l+ e av++r + GGt++e+v+ +i+e+k lcl|NCBI__GCF_000425265.1:WP_027722612.1 419 IDGDVFEILSYEAAVKRRVSPGGTGPESVKAQISELKD 456 **********************************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (459 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: 00:00:00.01 # Mc/sec: 11.61 // [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