Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate WP_044411616.1 NA59_RS09635 argininosuccinate synthase
Query= SwissProt::P59846 (400 letters) >NCBI__GCF_000934765.1:WP_044411616.1 Length = 405 Score = 506 bits (1303), Expect = e-148 Identities = 251/394 (63%), Positives = 305/394 (77%), Gaps = 4/394 (1%) Query: 2 KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIALDL 61 K+VLAYSGGLDTSII KWL++ Y+ EV+ FTADIGQGEEVE AR KA G + DL Sbjct: 6 KVVLAYSGGLDTSIIAKWLQDEYQCEVVTFTADIGQGEEVEPARAKAQAMGIKEIFIEDL 65 Query: 62 KEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGND 121 +EEF RDFVFPM RA A+YEG YLLGTSIARPLIAK LV IA++ A+AI+HGATGKGND Sbjct: 66 REEFARDFVFPMFRANAIYEGEYLLGTSIARPLIAKRLVEIAKDVNADAISHGATGKGND 125 Query: 122 QVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEK--PYSMDANLL 179 QVRFEL AYAL PD++VIAPWREW R++++ YAE H I + + K PYSMDANLL Sbjct: 126 QVRFELGAYALMPDVRVIAPWREWDLNSREKLMTYAEEHNIAIENKKGKKSPYSMDANLL 185 Query: 180 HISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALL 239 HISYEGGVLEDPW+EP + M+R + PE AP+ P Y+E+ + +GD VA+NG+ LSPA ++ Sbjct: 186 HISYEGGVLEDPWSEPEESMWRWSVSPENAPNEPTYIELTYEKGDIVALNGQALSPATIM 245 Query: 240 QRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRD 299 LN+IGG +G+GR D+VENRFVGMKSRG YETP GTI+ A RA+ES+TLDRE H +D Sbjct: 246 AELNKIGGANGIGRDDLVENRFVGMKSRGCYETPAGTIMIKAHRAIESITLDREAAHLKD 305 Query: 300 MLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPK-SLY 358 L P+YA+LVY GFW++PERE LQA D V GV RLKLYKGNV VVGRK+ SL+ Sbjct: 306 ELMPRYAKLVYNGFWFSPEREMLQAAIDKSQTVVNGVVRLKLYKGNVIVVGRKSESDSLF 365 Query: 359 RQDLVSF-DEAGGYDQKDAEGFIKIQALRLRVRA 391 + + +F D+ G Y+QKDAEGFIK+ ALRLR+ A Sbjct: 366 DESIATFEDDKGAYNQKDAEGFIKLNALRLRIAA 399 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: 499 Number of extensions: 14 Number of successful extensions: 3 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: 405 Length adjustment: 31 Effective length of query: 369 Effective length of database: 374 Effective search space: 138006 Effective search space used: 138006 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_044411616.1 NA59_RS09635 (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.17417.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-143 463.1 0.0 5.8e-143 462.9 0.0 1.0 1 lcl|NCBI__GCF_000934765.1:WP_044411616.1 NA59_RS09635 argininosuccinate s Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000934765.1:WP_044411616.1 NA59_RS09635 argininosuccinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 462.9 0.0 5.8e-143 5.8e-143 1 392 [. 6 401 .. 6 403 .. 0.96 Alignments for each domain: == domain 1 score: 462.9 bits; conditional E-value: 5.8e-143 TIGR00032 1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdy 68 kvvlaysGGlDts++ k+l+++ +ev+++t+d+Gq+ e+++ ++ ka ++G ++ + D reef++d+ lcl|NCBI__GCF_000934765.1:WP_044411616.1 6 KVVLAYSGGLDTSIIAKWLQDEyQCEVVTFTADIGQG-EEVEPARAKAQAMGIKEIFIEDLREEFARDF 73 8*********************999***********9.9****************************** PP TIGR00032 69 lfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkv 137 +f+ +ana+yeg+Yll+t++aRpliak+lve+ak+ +a+a++hG+tgKGnDqvRFel ++l pd++v lcl|NCBI__GCF_000934765.1:WP_044411616.1 74 VFPMFRANAIYEGEYLLGTSIARPLIAKRLVEIAKDVNADAISHGATGKGNDQVRFELGAYALMPDVRV 142 ********************************************************************* PP TIGR00032 138 iaPvreleli.ReeeieyaaekGievpve..kekaysiDenllgrsiEageLEdpsteppediyelvkd 203 iaP+re++l Re+++ ya+e+ i ++ + k+++ys+D nll++s+E+g LEdp++ep e ++++ ++ lcl|NCBI__GCF_000934765.1:WP_044411616.1 143 IAPWREWDLNsREKLMTYAEEHNIAIENKkgKKSPYSMDANLLHISYEGGVLEDPWSEPEESMWRWSVS 211 *********88**********98877665116789*********************************9 PP TIGR00032 204 piektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEap 272 p++++ +ep ++e+++ekG valng+ l+p +++ ++n+i+g++G+Gr D vE+R +g+KsR++YE+p lcl|NCBI__GCF_000934765.1:WP_044411616.1 212 PENAP-NEPTYIELTYEKGDIVALNGQALSPATIMAELNKIGGANGIGRDDLVENRFVGMKSRGCYETP 279 98888.9************************************************************** PP TIGR00032 273 alllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklf 341 a +++ikAh+++e+ +l+++ +++k+ +y++l+Y+G+wf+p++e+l+a+i+k+q v+G+vr+kl+ lcl|NCBI__GCF_000934765.1:WP_044411616.1 280 AGTIMIKAHRAIESITLDREAAHLKDELMPRYAKLVYNGFWFSPEREMLQAAIDKSQTVVNGVVRLKLY 348 ********************************************************************* PP TIGR00032 342 kGnaivigrk.seyslYdeelvsfek.dkefdqkdaiGfikirglqikvyrek 392 kGn+iv+grk + +sl+de +++fe + +++qkda+Gfik+++l+ ++ ++k lcl|NCBI__GCF_000934765.1:WP_044411616.1 349 KGNVIVVGRKsESDSLFDESIATFEDdKGAYNQKDAEGFIKLNALRLRIAARK 401 **********66689**********9445799*************99987766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (405 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: 12.20 // [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