Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate WP_092344188.1 BLU87_RS01650 argininosuccinate lyase
Query= BRENDA::Q8DVX5 (460 letters) >NCBI__GCF_900107645.1:WP_092344188.1 Length = 457 Score = 473 bits (1216), Expect = e-138 Identities = 234/449 (52%), Positives = 318/449 (70%) Query: 5 NHKLWGGRFEAGLAQWVEEFGASISFDQKLAEFDLKGSIAHVTMLGEKGIISQEDAATIK 64 N+KLWGGRF ++VEEF ASI F+Q+L +D++GS AH MLG + IIS+ DA I Sbjct: 3 NNKLWGGRFTQPTDKFVEEFTASIGFEQRLGSYDIQGSKAHAEMLGRQEIISEADAQKII 62 Query: 65 AGLEDLLEEYKAGQLKFDVSNEDIHMNMESLLTAKIGPVAGKLHTARSRNDQVATDMHLY 124 +GL+++L + ++G+++F ++ EDIHMN+E+ L +IGPV GKLHT RSRNDQVA D+ LY Sbjct: 63 SGLDEILNKIESGKMEFSIALEDIHMNIEAQLIERIGPVGGKLHTGRSRNDQVAVDIRLY 122 Query: 125 LKAKLDEVIEKLANLRTVLVDLADKHVHTIMPGYTHLQHAQPISFGHHLMAYYNMFTRDS 184 L+ ++D +++ L L L+ A+ ++ IMPGYTHLQ AQP+ + HH++AY M +RD Sbjct: 123 LRDEIDVILDYLKKLEAALIQQAENNLDIIMPGYTHLQTAQPVLYSHHMLAYREMISRDR 182 Query: 185 ERFIFNVKHTDLSPLGAAALAGTTFPIDREMTAQLMGFAEPYSNSLDAVSDRDFILEFLS 244 R +L PLGA ALAGTTFPIDRE TA+ +GF NSLD+VSDRDF +EF S Sbjct: 183 SRLRDLRARFNLMPLGAGALAGTTFPIDREWTAKRLGFDGVTRNSLDSVSDRDFAIEFCS 242 Query: 245 NASILMMHMSRMCEEVISWCSHEYQFVTLSDTFSTGSSIMPQKKNPDMAELIRGKSGRVY 304 ASILMMH+SR+ EE+I W S ++ F+ LSD F TGSSIMPQKKNPD+ EL+RGK+GRVY Sbjct: 243 FASILMMHLSRLSEELILWSSADFNFIELSDAFCTGSSIMPQKKNPDVPELVRGKTGRVY 302 Query: 305 ANLFGLLTVMKALPLAYNKDLQEDKEGMFDTAETITVALDILAGMLSSMIVNDKHMAEST 364 NL LLT+MK+LPLAYNKD+QEDKE +FDT +TI +L I A M+ M V +M + Sbjct: 303 GNLMALLTLMKSLPLAYNKDMQEDKEPLFDTIDTIKGSLKIFADMVVEMQVKGDNMRIAA 362 Query: 365 QKDFSNATELADYLASKGMPFRQAHEIVGKLILECSKNGHYLQDVPLERYQTISDLIEED 424 + FS AT++ADY KG+PFRQAHE+VGK + C + G + ++ L +Q+ SDLI D Sbjct: 363 ARGFSTATDVADYCVRKGLPFRQAHEVVGKTVRYCVETGKDIPELSLAEFQSFSDLITAD 422 Query: 425 VYETLKSHTAVERRHSLGGTGFEQVKWQI 453 +Y+ + +V R + GGT E V+ ++ Sbjct: 423 IYDYVTLEASVNARKATGGTAREAVEREL 451 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: 566 Number of extensions: 23 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: 457 Length adjustment: 33 Effective length of query: 427 Effective length of database: 424 Effective search space: 181048 Effective search space used: 181048 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_092344188.1 BLU87_RS01650 (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.24045.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-198 644.7 0.0 5.1e-198 644.6 0.0 1.0 1 lcl|NCBI__GCF_900107645.1:WP_092344188.1 BLU87_RS01650 argininosuccinate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900107645.1:WP_092344188.1 BLU87_RS01650 argininosuccinate lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 644.6 0.0 5.1e-198 5.1e-198 1 451 [. 6 455 .. 6 457 .] 0.99 Alignments for each domain: == domain 1 score: 644.6 bits; conditional E-value: 5.1e-198 TIGR00838 1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevke 69 lwggR+++ +dk v+ef+as+ f+++l ++Di+gs+ah+++L ++ i++e +a+k+i++L+e+ +++++ lcl|NCBI__GCF_900107645.1:WP_092344188.1 6 LWGGRFTQPTDKFVEEFTASIGFEQRLGSYDIQGSKAHAEMLGRQEIISEADAQKIISGLDEILNKIES 74 7******************************************************************** PP TIGR00838 70 gklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalv 138 gk+e++ eDiH+++E++li+++g vg+klhtgrsRnDqva+d+rlylrd+++ +++ lk+l +al+ lcl|NCBI__GCF_900107645.1:WP_092344188.1 75 GKMEFSIALEDIHMNIEAQLIERIG-PVGGKLHTGRSRNDQVAVDIRLYLRDEIDVILDYLKKLEAALI 142 *************************.******************************************* PP TIGR00838 139 ekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidr 207 ++Ae++ +++mpgytHLq AqP+ ++Hh+lay+em++rD +Rl d R n PlG+gAlagt+f+idr lcl|NCBI__GCF_900107645.1:WP_092344188.1 143 QQAENNLDIIMPGYTHLQTAQPVLYSHHMLAYREMISRDRSRLRDLRARFNLMPLGAGALAGTTFPIDR 211 ********************************************************************* PP TIGR00838 208 ellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgss 276 e +a+ LgFd v++nsld+vsdRDf+iE+ s a++lm+hlsrl+Eelil+ss++f+f+elsd++++gss lcl|NCBI__GCF_900107645.1:WP_092344188.1 212 EWTAKRLGFDGVTRNSLDSVSDRDFAIEFCSFASILMMHLSRLSEELILWSSADFNFIELSDAFCTGSS 280 ********************************************************************* PP TIGR00838 277 imPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllk 345 imPqKKnpDv El+Rgktgrv+Gnl++llt++K+lPlaYnkD+qEdke+lfd+++t++ +l++++ ++ lcl|NCBI__GCF_900107645.1:WP_092344188.1 281 IMPQKKNPDVPELVRGKTGRVYGNLMALLTLMKSLPLAYNKDMQEDKEPLFDTIDTIKGSLKIFADMVV 349 ********************************************************************* PP TIGR00838 346 elkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsek 414 e++v+ ++++ aa+++f++atd+Ady vrkG+PFR+ahe+vG++v++++e+Gk++ el+l+e+q +s lcl|NCBI__GCF_900107645.1:WP_092344188.1 350 EMQVKGDNMRIAAARGFSTATDVADYCVRKGLPFRQAHEVVGKTVRYCVETGKDIPELSLAEFQSFSDL 418 ********************************************************************* PP TIGR00838 415 leedvlevldleeavekrdakGGtakeevekaieeak 451 ++ d+++ ++le +v++r+a+GGta e+ve+ ++ ++ lcl|NCBI__GCF_900107645.1:WP_092344188.1 419 ITADIYDYVTLEASVNARKATGGTAREAVERELKRLQ 455 *******************************999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (457 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: 7.51 // [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