Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate WP_025274364.1 HALAL_RS0112715 argininosuccinate synthase
Query= SwissProt::P59846 (400 letters) >NCBI__GCF_000527155.1:WP_025274364.1 Length = 397 Score = 307 bits (787), Expect = 3e-88 Identities = 160/385 (41%), Positives = 242/385 (62%), Gaps = 3/385 (0%) Query: 2 KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQG-EEVEEAREKALRTGASKAIALD 60 +IVLAYSGGLDTS+ + +L E + AEVIA D GQG E++E ++AL GA A +D Sbjct: 4 RIVLAYSGGLDTSVAIPYLAEQFDAEVIAVAIDAGQGGEDLEAVHDRALGCGAVAAEVID 63 Query: 61 LKEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGN 120 +EEF ++ +P + A A+Y Y L ++++RPLI KHL + AE+ A ++HG TGKGN Sbjct: 64 AREEFAAEYCYPAVSANALYMDRYPLVSALSRPLIVKHLAQAAEKHDATIVSHGCTGKGN 123 Query: 121 DQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEKPYSMDANLLH 180 DQVRFE AL PD+K++AP R++++ R + I +AE +P+ VT PYS+D NL Sbjct: 124 DQVRFEAGLAALAPDLKIVAPARDFAWT-RDKAIVFAEEKNLPIDVTASSPYSIDQNLWG 182 Query: 181 ISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALLQ 240 + E G LED W P + ++ + P E D P+ V V F +G PVA++GE + L+ Sbjct: 183 RAVETGFLEDLWNAPIEDIYSYSHSPAEPAD-PDEVIVTFDKGRPVALDGETKTAYQLID 241 Query: 241 RLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRDM 300 LN G G+GR+D+VE+R VG+KSR VYE+P G L A +E++TL+RE + Sbjct: 242 ELNRRAGAQGIGRIDMVEDRLVGIKSREVYESPAGIALITAHMELEAVTLEREQARFKRT 301 Query: 301 LSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYRQ 360 + ++ E+VY G W++P + +L+++ D R V+G RL + G V GR + +SLY Sbjct: 302 VDQRWGEMVYDGLWFSPLKNSLESFIDDTQRHVSGDIRLHMQHGKATVTGRHSHQSLYDF 361 Query: 361 DLVSFDEAGGYDQKDAEGFIKIQAL 385 +L ++DE + Q+ A GF+++ +L Sbjct: 362 NLATYDEGDSFKQEHARGFVELWSL 386 Lambda K H 0.319 0.137 0.402 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: 383 Number of extensions: 10 Number of successful extensions: 4 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: 400 Length of database: 397 Length adjustment: 31 Effective length of query: 369 Effective length of database: 366 Effective search space: 135054 Effective search space used: 135054 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_025274364.1 HALAL_RS0112715 (argininosuccinate synthase)
to HMM TIGR00032 (argG: argininosuccinate synthase (EC 6.3.4.5))
# 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/TIGR00032.hmm # target sequence database: /tmp/gapView.28274.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00032 [M=394] Accession: TIGR00032 Description: argG: argininosuccinate synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-146 474.8 0.0 1.6e-146 474.6 0.0 1.0 1 lcl|NCBI__GCF_000527155.1:WP_025274364.1 HALAL_RS0112715 argininosuccinat Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000527155.1:WP_025274364.1 HALAL_RS0112715 argininosuccinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 474.6 0.0 1.6e-146 1.6e-146 1 389 [. 4 391 .. 4 396 .. 0.99 Alignments for each domain: == domain 1 score: 474.6 bits; conditional E-value: 1.6e-146 TIGR00032 1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdy 68 ++vlaysGGlDtsva+++l e+ aeviav++d Gq+ edl+a++ +al +Ga+ a viDareef+++y lcl|NCBI__GCF_000527155.1:WP_025274364.1 4 RIVLAYSGGLDTSVAIPYLAEQfDAEVIAVAIDAGQGGEDLEAVHDRALGCGAVAAEVIDAREEFAAEY 72 69******************************************************************* PP TIGR00032 69 lfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkv 137 +a+ ana+y ++Y+l++aL+Rpli k l ++a+k++a++v+hGctgKGnDqvRFe+ + +l+pdlk+ lcl|NCBI__GCF_000527155.1:WP_025274364.1 73 CYPAVSANALYMDRYPLVSALSRPLIVKHLAQAAEKHDATIVSHGCTGKGNDQVRFEAGLAALAPDLKI 141 ********************************************************************* PP TIGR00032 138 iaPvreleliReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdpie 206 +aP+r+ ++R + i +a+ek +++ v+ +++ysiD+nl+gr++E+g LEd++ +p+ediy++ +p e lcl|NCBI__GCF_000527155.1:WP_025274364.1 142 VAPARDFAWTRDKAIVFAEEKNLPIDVTASSPYSIDQNLWGRAVETGFLEDLWNAPIEDIYSYSHSPAE 210 *****************************************************************8877 PP TIGR00032 207 ktedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapall 275 +p++v ++F+kG Pval+ge+ ++ +li ++n+ ag++G+GriD+vEdR++g+KsRe+YE pa + lcl|NCBI__GCF_000527155.1:WP_025274364.1 211 PA--DPDEVIVTFDKGRPVALDGETKTAYQLIDELNRRAGAQGIGRIDMVEDRLVGIKSREVYESPAGI 277 66..99*************************************************************** PP TIGR00032 276 lLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkGn 344 Li+Ah +Le +l++++++fk++v+++++e++Y Glwf+pl++ l+++i+ tq++v+G +r+++ +G+ lcl|NCBI__GCF_000527155.1:WP_025274364.1 278 ALITAHMELEAVTLEREQARFKRTVDQRWGEMVYDGLWFSPLKNSLESFIDDTQRHVSGDIRLHMQHGK 346 ********************************************************************* PP TIGR00032 345 aivigrkseyslYdeelvsfekdkefdqkdaiGfikirglqikvy 389 a+v gr+s++slYd +l+++++ ++f+q++a Gf+++++l++k lcl|NCBI__GCF_000527155.1:WP_025274364.1 347 ATVTGRHSHQSLYDFNLATYDEGDSFKQEHARGFVELWSLPAKLA 391 ****************************************99864 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (397 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: 00:00:00.01 # Mc/sec: 9.35 // [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