Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate WP_092054523.1 BQ4888_RS05185 argininosuccinate synthase
Query= SwissProt::P59846 (400 letters) >NCBI__GCF_900111775.1:WP_092054523.1 Length = 406 Score = 510 bits (1313), Expect = e-149 Identities = 246/392 (62%), Positives = 309/392 (78%), Gaps = 1/392 (0%) Query: 2 KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIALDL 61 K+VLAYSGGLDTSIILKWL E Y EV+A++AD+GQGEE++ EKA +TGAS +DL Sbjct: 9 KVVLAYSGGLDTSIILKWLTEEYDCEVVAYSADLGQGEELDFIPEKAKKTGASSCHIVDL 68 Query: 62 KEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGND 121 KEEF RDFVFPM RA A+YEG Y LGTSIARPLIAK + IA +EGA+A++HGATGKGND Sbjct: 69 KEEFARDFVFPMFRANAIYEGRYFLGTSIARPLIAKAQMEIAAKEGADAVSHGATGKGND 128 Query: 122 QVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEKPYSMDANLLHI 181 QVRFE+ Y P IKVIAPWREW + R ++ YA+ HGIPVP +++ P+S D NLLHI Sbjct: 129 QVRFEIAYYHYDPAIKVIAPWREWDMKSRTDLENYAKKHGIPVPTSKKFPWSSDRNLLHI 188 Query: 182 SYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALLQR 241 S+EG +LE+PWAE P+ M+++T PE+APD PEYVE+EF +GD VAVNG RLSPA LL + Sbjct: 189 SFEGDILENPWAEAPEEMYQLTVRPEDAPDQPEYVEIEFEKGDAVAVNGVRLSPAKLLAK 248 Query: 242 LNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRDML 301 LNE GG+HG+GRVD++ENR+VGMKSRGVYETPGGTIL A RAVES+ +DREV+H RD L Sbjct: 249 LNEFGGKHGIGRVDLLENRYVGMKSRGVYETPGGTILEEAHRAVESICMDREVMHLRDSL 308 Query: 302 SPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGR-KAPKSLYRQ 360 P+YA+++Y G+W++PER+ LQ D ++V G AR+KLYKG+ VVGR A SL+ Sbjct: 309 VPRYADMIYNGYWFSPERQVLQTLIDASQQTVNGKARIKLYKGHCRVVGRDSASDSLFNV 368 Query: 361 DLVSFDEAGGYDQKDAEGFIKIQALRLRVRAL 392 D +F++ Y+Q DAEGFIK+ ALRLR+ A+ Sbjct: 369 DFATFEKDDVYNQADAEGFIKLNALRLRIAAI 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: 516 Number of extensions: 12 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_092054523.1 BQ4888_RS05185 (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.18828.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.7e-150 485.5 0.0 9.4e-150 485.2 0.0 1.0 1 lcl|NCBI__GCF_900111775.1:WP_092054523.1 BQ4888_RS05185 argininosuccinate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900111775.1:WP_092054523.1 BQ4888_RS05185 argininosuccinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 485.2 0.0 9.4e-150 9.4e-150 1 389 [. 9 398 .. 9 403 .. 0.98 Alignments for each domain: == domain 1 score: 485.2 bits; conditional E-value: 9.4e-150 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_900111775.1:WP_092054523.1 9 KVVLAYSGGLDTSIILKWLTEEyDCEVVAYSADLGQG-EELDFIPEKAKKTGASSCHIVDLKEEFARDF 76 8*********************999***********9.9****************************** PP TIGR00032 69 lfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkv 137 +f+ +ana+yeg+Y+l+t++aRpliak+++e+a kega+av+hG+tgKGnDqvRFe+ + +p +kv lcl|NCBI__GCF_900111775.1:WP_092054523.1 77 VFPMFRANAIYEGRYFLGTSIARPLIAKAQMEIAAKEGADAVSHGATGKGNDQVRFEIAYYHYDPAIKV 145 ********************************************************************* PP TIGR00032 138 iaPvreleli.ReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdpi 205 iaP+re+++ R+++ +ya+++Gi+vp++k+ ++s D+nll++s E+++LE+p++e pe++y+l++ p+ lcl|NCBI__GCF_900111775.1:WP_092054523.1 146 IAPWREWDMKsRTDLENYAKKHGIPVPTSKKFPWSSDRNLLHISFEGDILENPWAEAPEEMYQLTVRPE 214 *********88*******************************************************988 PP TIGR00032 206 ektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapal 274 +++ d+pe+veieFekG va+ng++l+p +l+ k+ne +gkhG+Gr+D +E+R++g+KsR++YE+p+ lcl|NCBI__GCF_900111775.1:WP_092054523.1 215 DAP-DQPEYVEIEFEKGDAVAVNGVRLSPAKLLAKLNEFGGKHGIGRVDLLENRYVGMKSRGVYETPGG 282 887.***************************************************************** PP TIGR00032 275 llLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkG 343 ++L +Ah+++e+ ++++v+++++ +y+ +iY+G+wf+p+++ l++li+ +q+ v+G r+kl+kG lcl|NCBI__GCF_900111775.1:WP_092054523.1 283 TILEEAHRAVESICMDREVMHLRDSLVPRYADMIYNGYWFSPERQVLQTLIDASQQTVNGKARIKLYKG 351 ********************************************************************* PP TIGR00032 344 naivigrk.seyslYdeelvsfekdkefdqkdaiGfikirglqikvy 389 + +v+gr+ +sl++ + ++fekd+ ++q da+Gfik+++l+ ++ lcl|NCBI__GCF_900111775.1:WP_092054523.1 352 HCRVVGRDsASDSLFNVDFATFEKDDVYNQADAEGFIKLNALRLRIA 398 ********7789******************************98765 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: 00:00:00.02 # Mc/sec: 7.87 // [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