Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate WP_074201126.1 BUQ81_RS04120 argininosuccinate synthase
Query= SwissProt::P59846 (400 letters) >NCBI__GCF_900141795.1:WP_074201126.1 Length = 403 Score = 533 bits (1373), Expect = e-156 Identities = 262/397 (65%), Positives = 311/397 (78%), Gaps = 3/397 (0%) Query: 2 KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIALDL 61 K+VLAYSGGLDTSII KWL+E Y EV+ FTADIGQGEEVE AREKA G + DL Sbjct: 7 KVVLAYSGGLDTSIIAKWLQEAYDCEVVTFTADIGQGEEVEPAREKAQAMGIREIYIEDL 66 Query: 62 KEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGND 121 +EEF RD+V+PM RA A+YEG YLLGTSIARPLIAK LV IAEE GA+AIAHGATGKGND Sbjct: 67 REEFARDYVYPMFRANAIYEGEYLLGTSIARPLIAKRLVEIAEETGADAIAHGATGKGND 126 Query: 122 QVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEK--PYSMDANLL 179 QVRFEL AYAL PDIKVIAPWREW R++++AYAE HGIP+ + K PYSMDANLL Sbjct: 127 QVRFELNAYALNPDIKVIAPWREWDLNSREKLMAYAETHGIPIENKKGKKSPYSMDANLL 186 Query: 180 HISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALL 239 HISYEGG+LEDPW EP + M+R T PE+AP+ P Y+E+ + +GD V +NGER++PA ++ Sbjct: 187 HISYEGGLLEDPWNEPEESMWRWTVSPEKAPNEPVYLELAYEKGDLVGINGERMTPAQVM 246 Query: 240 QRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRD 299 + LN IGG HG+GR DIVENRFVGMKSRG YETP GTI+ A RA+ES+TLDRE H +D Sbjct: 247 ETLNRIGGEHGIGRTDIVENRFVGMKSRGCYETPAGTIMLKAHRAIESITLDREAAHTKD 306 Query: 300 MLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYR 359 L P+YA L+Y GFW+APERE LQA D + VTG R+KLYKGNV VVGRK+P SL+ Sbjct: 307 ELMPRYATLIYNGFWFAPEREMLQAAIDQTQQYVTGTVRVKLYKGNVIVVGRKSPYSLFD 366 Query: 360 QDLVSF-DEAGGYDQKDAEGFIKIQALRLRVRALVER 395 + + +F D+ G YDQKDAEGFIK+ ALRL+ A +R Sbjct: 367 EKIATFEDDEGAYDQKDAEGFIKLNALRLKNLAKRQR 403 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: 528 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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_074201126.1 BUQ81_RS04120 (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.4897.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-152 493.3 0.0 3.6e-152 493.2 0.0 1.0 1 lcl|NCBI__GCF_900141795.1:WP_074201126.1 BUQ81_RS04120 argininosuccinate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900141795.1:WP_074201126.1 BUQ81_RS04120 argininosuccinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 493.2 0.0 3.6e-152 3.6e-152 1 392 [. 7 401 .. 7 403 .] 0.97 Alignments for each domain: == domain 1 score: 493.2 bits; conditional E-value: 3.6e-152 TIGR00032 1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdy 68 kvvlaysGGlDts++ k+l+e +ev+++t+d+Gq+ e+++ ++eka ++G + y+ D reef++dy lcl|NCBI__GCF_900141795.1:WP_074201126.1 7 KVVLAYSGGLDTSIIAKWLQEAyDCEVVTFTADIGQG-EEVEPAREKAQAMGIREIYIEDLREEFARDY 74 8*********************999***********9.9****************************** PP TIGR00032 69 lfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkv 137 + + +ana+yeg+Yll+t++aRpliak+lve+a++ ga+a+ahG+tgKGnDqvRFel ++lnpd+kv lcl|NCBI__GCF_900141795.1:WP_074201126.1 75 VYPMFRANAIYEGEYLLGTSIARPLIAKRLVEIAEETGADAIAHGATGKGNDQVRFELNAYALNPDIKV 143 ********************************************************************* PP TIGR00032 138 iaPvreleli.ReeeieyaaekGievpvek..ekaysiDenllgrsiEageLEdpsteppediyelvkd 203 iaP+re++l Re++++ya+++Gi+++ +k +++ys+D nll++s+E+g LEdp+ ep e +++++++ lcl|NCBI__GCF_900141795.1:WP_074201126.1 144 IAPWREWDLNsREKLMAYAETHGIPIENKKgkKSPYSMDANLLHISYEGGLLEDPWNEPEESMWRWTVS 212 *********88**************9887522679*********************************9 PP TIGR00032 204 piektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEap 272 p++++ +ep ++e+++ekG v +nge+++p ++++++n+i+g+hG+Gr+DivE+R +g+KsR++YE+p lcl|NCBI__GCF_900141795.1:WP_074201126.1 213 PEKAP-NEPVYLELAYEKGDLVGINGERMTPAQVMETLNRIGGEHGIGRTDIVENRFVGMKSRGCYETP 280 98887.9************************************************************** PP TIGR00032 273 alllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklf 341 a ++++kAh+++e+ +l+++ ++ k+ +y+ liY+G+wf p++e+l+a+i++tq+ vtGtvrvkl+ lcl|NCBI__GCF_900141795.1:WP_074201126.1 281 AGTIMLKAHRAIESITLDREAAHTKDELMPRYATLIYNGFWFAPEREMLQAAIDQTQQYVTGTVRVKLY 349 ********************************************************************* PP TIGR00032 342 kGnaivigrkseyslYdeelvsfek.dkefdqkdaiGfikirglqikvyrek 392 kGn+iv+grks+ysl+de++++fe + ++dqkda+Gfik+++l+ k+ +++ lcl|NCBI__GCF_900141795.1:WP_074201126.1 350 KGNVIVVGRKSPYSLFDEKIATFEDdEGAYDQKDAEGFIKLNALRLKNLAKR 401 ************************956689***************9987765 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.70 // [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