Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate WP_092344190.1 BLU87_RS01660 argininosuccinate synthase
Query= SwissProt::P59846 (400 letters) >NCBI__GCF_900107645.1:WP_092344190.1 Length = 406 Score = 520 bits (1338), Expect = e-152 Identities = 251/392 (64%), Positives = 309/392 (78%), Gaps = 1/392 (0%) Query: 2 KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIALDL 61 K+VLAYSGGLDTSIILKWL E Y+ EV+AF+AD+GQGEE++ EKA +TGAS LDL Sbjct: 9 KVVLAYSGGLDTSIILKWLVEEYQCEVVAFSADLGQGEELDHIPEKAKKTGASSCHILDL 68 Query: 62 KEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGND 121 KEEF RDFVFPM RA A+YEG Y LGTSIARPLI+K + IA +EGA+A++HGATGKGND Sbjct: 69 KEEFTRDFVFPMFRANAIYEGRYFLGTSIARPLISKAQMEIAAKEGADAVSHGATGKGND 128 Query: 122 QVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEKPYSMDANLLHI 181 QVRFE++ Y P +KVIAPWREW R + AYA+ H IP+P ++ P+S D NLLHI Sbjct: 129 QVRFEVSYYHFNPAVKVIAPWREWDLNSRTALEAYAKKHAIPIPTNKKVPWSSDRNLLHI 188 Query: 182 SYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALLQR 241 S+EG LEDPWAE P+ M+ +T PE+APD PEY+EVEF +GD VA+NGERLSPA LL + Sbjct: 189 SFEGYALEDPWAEAPEEMYTLTVAPEDAPDQPEYIEVEFEKGDAVAINGERLSPANLLAK 248 Query: 242 LNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRDML 301 LN++GG+HG+GRVD++ENR+VGMKSRGVYETPGGTIL A RAVES+T+DREV+H RD L Sbjct: 249 LNQLGGKHGIGRVDLMENRYVGMKSRGVYETPGGTILEEAHRAVESITMDREVMHLRDSL 308 Query: 302 SPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGR-KAPKSLYRQ 360 P+YAE++Y G+W+APER ALQA D ++V G AR+KLYKG+ VVGR A SL+ Sbjct: 309 VPRYAEMIYNGYWFAPERIALQALIDETQKTVNGKARIKLYKGHCRVVGRDSATDSLFNV 368 Query: 361 DLVSFDEAGGYDQKDAEGFIKIQALRLRVRAL 392 D +F+ Y+Q DAEGFIKI ALRLR+ A+ Sbjct: 369 DFATFEADEVYNQADAEGFIKINALRLRIAAM 400 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: 521 Number of extensions: 15 Number of successful extensions: 2 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: 406 Length adjustment: 31 Effective length of query: 369 Effective length of database: 375 Effective search space: 138375 Effective search space used: 138375 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_092344190.1 BLU87_RS01660 (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.10614.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-148 479.5 0.0 5.9e-148 479.3 0.0 1.0 1 lcl|NCBI__GCF_900107645.1:WP_092344190.1 BLU87_RS01660 argininosuccinate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900107645.1:WP_092344190.1 BLU87_RS01660 argininosuccinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 479.3 0.0 5.9e-148 5.9e-148 1 390 [. 9 399 .. 9 403 .. 0.98 Alignments for each domain: == domain 1 score: 479.3 bits; conditional E-value: 5.9e-148 TIGR00032 1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdy 68 kvvlaysGGlDts++lk+l e+ +ev+a+ +d+Gq+ e+ld+i+eka+k Ga ++D +eef +d+ lcl|NCBI__GCF_900107645.1:WP_092344190.1 9 KVVLAYSGGLDTSIILKWLVEEyQCEVVAFSADLGQG-EELDHIPEKAKKTGASSCHILDLKEEFTRDF 76 8*********************899***********9.9****************************** PP TIGR00032 69 lfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkv 137 +f+ +ana+yeg+Y+l+t++aRpli+k+++e+a kega+av+hG+tgKGnDqvRFe+s + np +kv lcl|NCBI__GCF_900107645.1:WP_092344190.1 77 VFPMFRANAIYEGRYFLGTSIARPLISKAQMEIAAKEGADAVSHGATGKGNDQVRFEVSYYHFNPAVKV 145 ********************************************************************* PP TIGR00032 138 iaPvreleli.ReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdpi 205 iaP+re++l R+ + +ya+++ i++p++k+ ++s D+nll++s E+ LEdp++e pe++y+l++ p+ lcl|NCBI__GCF_900107645.1:WP_092344190.1 146 IAPWREWDLNsRTALEAYAKKHAIPIPTNKKVPWSSDRNLLHISFEGYALEDPWAEAPEEMYTLTVAPE 214 *********88999****************************************************887 PP TIGR00032 206 ektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapal 274 +++ d+pe++e+eFekG va+nge+l+p +l+ k+n+++gkhG+Gr+D +E+R++g+KsR++YE+p+ lcl|NCBI__GCF_900107645.1:WP_092344190.1 215 DAP-DQPEYIEVEFEKGDAVAINGERLSPANLLAKLNQLGGKHGIGRVDLMENRYVGMKSRGVYETPGG 282 777.***************************************************************** PP TIGR00032 275 llLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkG 343 ++L +Ah+++e+ +++++v+++++ +y+e+iY+G+wf p++ al+ali++tq+ v+G r+kl+kG lcl|NCBI__GCF_900107645.1:WP_092344190.1 283 TILEEAHRAVESITMDREVMHLRDSLVPRYAEMIYNGYWFAPERIALQALIDETQKTVNGKARIKLYKG 351 ********************************************************************* PP TIGR00032 344 naivigrk.seyslYdeelvsfekdkefdqkdaiGfikirglqikvyr 390 + +v+gr+ ++sl++ + ++fe d+ ++q da+Gfiki++l+ ++ + lcl|NCBI__GCF_900107645.1:WP_092344190.1 352 HCRVVGRDsATDSLFNVDFATFEADEVYNQADAEGFIKINALRLRIAA 399 ********7899******************************988765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (406 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: 10.05 // [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