Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate 8499268 DvMF_0047 argininosuccinate synthase (RefSeq)
Query= SwissProt::P59846 (400 letters) >FitnessBrowser__Miya:8499268 Length = 401 Score = 505 bits (1301), Expect = e-148 Identities = 242/387 (62%), Positives = 296/387 (76%), Gaps = 1/387 (0%) Query: 2 KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIALDL 61 K+VLAYSGGLDTS+ILKW+ TY EV+ TAD+GQ E+++ KALRTGAS+A DL Sbjct: 7 KVVLAYSGGLDTSVILKWIAVTYGCEVVTLTADLGQEEDLDGVDAKALRTGASRAYVEDL 66 Query: 62 KEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGND 121 +EEF RDF+FPMMR+GAVYEG YLLGTSIARPLIAK LV IA EGA+A+AHGATGKGND Sbjct: 67 REEFARDFIFPMMRSGAVYEGRYLLGTSIARPLIAKRLVDIARAEGAQAVAHGATGKGND 126 Query: 122 QVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEKPYSMDANLLHI 181 QVRFEL AL PD+ VIAPWR W + R ++ A+AE HGIP+ T K YSMD N+LH Sbjct: 127 QVRFELAVNALAPDLDVIAPWRIWDLRSRTDLTAFAEQHGIPLS-TSSKQYSMDRNMLHC 185 Query: 182 SYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALLQR 241 S+EGG LEDPW EP M E+APD PEY+ +EF +GD VAVNGE +SPA++++ Sbjct: 186 SFEGGELEDPWCEPGPNSHVMAVPVEQAPDTPEYITIEFKKGDAVAVNGEAMSPASIIRT 245 Query: 242 LNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRDML 301 LN IGGRHG+GR+D+VENRFVG+KSRGVYETPGGT+L+ A R +E + +DRE +H RD L Sbjct: 246 LNTIGGRHGIGRLDMVENRFVGIKSRGVYETPGGTVLHIAHRDLEGICMDRESMHLRDQL 305 Query: 302 SPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYRQD 361 P+Y+E VY GFW+APEREA+QA+ D +V G RLKLYKGN Y VGR +P +LY D Sbjct: 306 IPRYSEAVYNGFWFAPEREAMQAFIDKTQETVNGTVRLKLYKGNAYPVGRTSPNTLYCHD 365 Query: 362 LVSFDEAGGYDQKDAEGFIKIQALRLR 388 L +F++ YD DA GFIK+Q LR+R Sbjct: 366 LATFEDCATYDHADAAGFIKLQGLRVR 392 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: 473 Number of extensions: 16 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: 401 Length adjustment: 31 Effective length of query: 369 Effective length of database: 370 Effective search space: 136530 Effective search space used: 136530 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 8499268 DvMF_0047 (argininosuccinate synthase (RefSeq))
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.13306.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.9e-152 491.9 0.0 1e-151 491.6 0.0 1.0 1 lcl|FitnessBrowser__Miya:8499268 DvMF_0047 argininosuccinate synt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8499268 DvMF_0047 argininosuccinate synthase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 491.6 0.0 1e-151 1e-151 1 393 [. 7 398 .. 7 399 .. 0.99 Alignments for each domain: == domain 1 score: 491.6 bits; conditional E-value: 1e-151 TIGR00032 1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdylfaaiqan 76 kvvlaysGGlDtsv+lk++ g+ev+++t+d+Gq eedld ++ kal+ Ga +ayv D reef++d++f+ ++ + lcl|FitnessBrowser__Miya:8499268 7 KVVLAYSGGLDTSVILKWIAVTyGCEVVTLTADLGQ-EEDLDGVDAKALRTGASRAYVEDLREEFARDFIFPMMRSG 82 8*******************999*************.8*************************************** PP TIGR00032 77 avyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvreleli.Reeei 152 avyeg+Yll+t++aRpliak+lv++a+ ega+avahG+tgKGnDqvRFel + +l+pdl+viaP+r ++l R+++ lcl|FitnessBrowser__Miya:8499268 83 AVYEGRYLLGTSIARPLIAKRLVDIARAEGAQAVAHGATGKGNDQVRFELAVNALAPDLDVIAPWRIWDLRsRTDLT 159 **********************************************************************88***** PP TIGR00032 153 eyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdpiektedepevveieFekGvPvalng 229 ++a+++Gi++ ++ +k+ys+D+n+l+ s E+geLEdp+ ep + + + + p+e+ +d+pe+++ieF+kG va+ng lcl|FitnessBrowser__Miya:8499268 160 AFAEQHGIPLSTS-SKQYSMDRNMLHCSFEGGELEDPWCEPGPNSHVMAV-PVEQAPDTPEYITIEFKKGDAVAVNG 234 **********998.6**************************999998888.99************************ PP TIGR00032 230 eslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLetlvltkdvlefkeiveekyse 306 e ++p +i+++n i+g+hG+Gr+D+vE+R +g+KsR++YE+p+ ++L++Ah+dLe ++++ +++++ +yse lcl|FitnessBrowser__Miya:8499268 235 EAMSPASIIRTLNTIGGRHGIGRLDMVENRFVGIKSRGVYETPGGTVLHIAHRDLEGICMDRESMHLRDQLIPRYSE 311 ***************************************************************************** PP TIGR00032 307 liYkGlwfdplaealdalikktqervtGtvrvklfkGnaivigrkseyslYdeelvsfekdkefdqkdaiGfikirg 383 +Y+G+wf p++ea++a+i+ktqe v+Gtvr+kl+kGna+ +gr+s+++lY ++l++fe +++d+ da+Gfik++g lcl|FitnessBrowser__Miya:8499268 312 AVYNGFWFAPEREAMQAFIDKTQETVNGTVRLKLYKGNAYPVGRTSPNTLYCHDLATFEDCATYDHADAAGFIKLQG 388 ***************************************************************************** PP TIGR00032 384 lqikvyrekl 393 l+++ y++++ lcl|FitnessBrowser__Miya:8499268 389 LRVRGYAQRV 398 ****999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (401 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9.21 // [ok]
This GapMind analysis is from Apr 09 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