Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate WP_029908482.1 P166_RS0102640 argininosuccinate synthase
Query= SwissProt::P59846 (400 letters) >NCBI__GCF_000711315.1:WP_029908482.1 Length = 403 Score = 498 bits (1281), Expect = e-145 Identities = 248/393 (63%), Positives = 300/393 (76%), Gaps = 3/393 (0%) Query: 2 KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIALDL 61 K+VLAYSGGLDTSII KWL+E Y+ EV+ FTADIGQGEEVE AR KA G + DL Sbjct: 6 KVVLAYSGGLDTSIIAKWLQEEYQCEVVTFTADIGQGEEVEPARAKAEAMGIKEIYIEDL 65 Query: 62 KEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGND 121 +EEF RDFVFPMMRA A+YEG Y LGTSIARPLI+K LV IA E GA+AI+HGATGKGND Sbjct: 66 REEFARDFVFPMMRANAIYEGEYRLGTSIARPLISKRLVEIARETGADAISHGATGKGND 125 Query: 122 QVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEK--PYSMDANLL 179 QVRFEL AYAL PD+KVIAPWREW R++++AYAE H I + + K PYSMDANLL Sbjct: 126 QVRFELNAYALMPDVKVIAPWREWDLLSREKLMAYAEEHNISIEKKKGKKSPYSMDANLL 185 Query: 180 HISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALL 239 HISYEGG++E+P EP + M+ T PE APD Y+ + F +GD V++NGE++SPA ++ Sbjct: 186 HISYEGGIIENPENEPEEDMWLWTVSPENAPDEATYLTIGFEKGDIVSINGEKMSPATVM 245 Query: 240 QRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRD 299 + LN++GG +G+GR DIVENRFVGMK+RG YETP GTI+ A RA+ESLTLDR H +D Sbjct: 246 EYLNQVGGANGIGRDDIVENRFVGMKARGCYETPAGTIMLKAHRAMESLTLDRNAAHLKD 305 Query: 300 MLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYR 359 L PKYAE++Y GFW+ PERE LQA D + VTG RLKLYKGNV VVGR + SL+ Sbjct: 306 ELMPKYAEMIYNGFWFTPEREMLQALIDASQKFVTGEVRLKLYKGNVVVVGRSSEFSLFD 365 Query: 360 QDLVSFDEAGG-YDQKDAEGFIKIQALRLRVRA 391 + + +F+E GG Y+ KDAEGFIK+ ALRLR A Sbjct: 366 EAIATFEEDGGAYNHKDAEGFIKLNALRLRTAA 398 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: 496 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: 403 Length adjustment: 31 Effective length of query: 369 Effective length of database: 372 Effective search space: 137268 Effective search space used: 137268 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_029908482.1 P166_RS0102640 (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.8434.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-145 470.5 0.1 3.3e-145 470.2 0.1 1.0 1 lcl|NCBI__GCF_000711315.1:WP_029908482.1 P166_RS0102640 argininosuccinate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000711315.1:WP_029908482.1 P166_RS0102640 argininosuccinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 470.2 0.1 3.3e-145 3.3e-145 1 390 [. 6 398 .. 6 402 .. 0.97 Alignments for each domain: == domain 1 score: 470.2 bits; conditional E-value: 3.3e-145 TIGR00032 1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdy 68 kvvlaysGGlDts++ k+l+e+ +ev+++t+d+Gq+ e+++ ++ ka ++G ++ y+ D reef++d+ lcl|NCBI__GCF_000711315.1:WP_029908482.1 6 KVVLAYSGGLDTSIIAKWLQEEyQCEVVTFTADIGQG-EEVEPARAKAEAMGIKEIYIEDLREEFARDF 73 8*********************899***********9.9****************************** PP TIGR00032 69 lfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkv 137 +f+ ++ana+yeg+Y l+t++aRpli+k+lve+a++ ga+a++hG+tgKGnDqvRFel ++l pd+kv lcl|NCBI__GCF_000711315.1:WP_029908482.1 74 VFPMMRANAIYEGEYRLGTSIARPLISKRLVEIARETGADAISHGATGKGNDQVRFELNAYALMPDVKV 142 ********************************************************************* PP TIGR00032 138 iaPvreleli.ReeeieyaaekGievpve..kekaysiDenllgrsiEageLEdpsteppediyelvkd 203 iaP+re++l Re++++ya+e+ i ++ + k+++ys+D nll++s+E+g++E+p+ ep ed++ ++++ lcl|NCBI__GCF_000711315.1:WP_029908482.1 143 IAPWREWDLLsREKLMAYAEEHNISIEKKkgKKSPYSMDANLLHISYEGGIIENPENEPEEDMWLWTVS 211 ********987**********99887766115779*********************************9 PP TIGR00032 204 piektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEap 272 p++++ de+ +++i+FekG v++nge+++p ++++ +n+++g++G+Gr DivE+R +g+K+R++YE+p lcl|NCBI__GCF_000711315.1:WP_029908482.1 212 PENAP-DEATYLTIGFEKGDIVSINGEKMSPATVMEYLNQVGGANGIGRDDIVENRFVGMKARGCYETP 279 98888.9************************************************************** PP TIGR00032 273 alllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklf 341 a ++++kAh+++e+l+l+++ +++k+ ky+e+iY+G+wf p++e+l+ali+ +q+ vtG+vr+kl+ lcl|NCBI__GCF_000711315.1:WP_029908482.1 280 AGTIMLKAHRAMESLTLDRNAAHLKDELMPKYAEMIYNGFWFTPEREMLQALIDASQKFVTGEVRLKLY 348 ********************************************************************* PP TIGR00032 342 kGnaivigrkseyslYdeelvsfek.dkefdqkdaiGfikirglqikvyr 390 kGn++v+gr+se sl+de +++fe+ ++++kda+Gfik+++l+ ++ + lcl|NCBI__GCF_000711315.1:WP_029908482.1 349 KGNVVVVGRSSEFSLFDEAIATFEEdGGAYNHKDAEGFIKLNALRLRTAA 398 ************************945689**************988765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (403 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: 8.81 // [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