Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate Dsui_3248 Dsui_3248 argininosuccinate synthase
Query= SwissProt::P59846 (400 letters) >FitnessBrowser__PS:Dsui_3248 Length = 409 Score = 509 bits (1310), Expect = e-149 Identities = 257/404 (63%), Positives = 313/404 (77%), Gaps = 8/404 (1%) Query: 2 KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIAL-- 59 K+VLAYSGGLDTS+ILKWL++TY+ EV+ FTAD+GQGEE+E AR KAL+ G Sbjct: 6 KVVLAYSGGLDTSVILKWLQDTYQCEVVTFTADLGQGEELEPARTKALKFGIKPENIFID 65 Query: 60 DLKEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKG 119 DL+EEFVRDFVFPM RA VYEG YLLGTSIARPLIAK L+ I GA+AI+HGATGKG Sbjct: 66 DLREEFVRDFVFPMFRANTVYEGEYLLGTSIARPLIAKRLIEITNLTGADAISHGATGKG 125 Query: 120 NDQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEK---PYSMDA 176 NDQVRFEL AYALKP +KVIAPWREW R++++AYAE HGIPV + ++ PYSMDA Sbjct: 126 NDQVRFELGAYALKPGVKVIAPWREWDLLSREKLLAYAEQHGIPVEMKHKQGGSPYSMDA 185 Query: 177 NLLHISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPA 236 NLLHISYEG LE+P AE + M+R T PE APDA EY+++EF +GD VA+NG+ + Sbjct: 186 NLLHISYEGRHLENPAAEAEEDMWRWTVSPENAPDAAEYLDLEFVQGDLVAINGQNMKAH 245 Query: 237 ALLQRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLH 296 LL +LNE+GG+HG+GR+D+VENR+VGMKSRG YETPGGTIL A RA+ES+TLDREV H Sbjct: 246 ELLAKLNELGGKHGIGRLDLVENRYVGMKSRGCYETPGGTILLRAHRAIESITLDREVAH 305 Query: 297 QRDMLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKA-PK 355 +D L P+YA LVY G+W+APER+ALQ DH ++V G RLKLYKGNV VVGR + Sbjct: 306 LKDDLMPRYASLVYNGYWWAPERKALQTLIDHTQQTVNGTVRLKLYKGNVIVVGRDSKTD 365 Query: 356 SLYRQDLVSF-DEAGGYDQKDAEGFIKIQALRLRVRA-LVEREG 397 SL+ + +F D+AG YDQKDA GFIK+ ALR+R+ A L R+G Sbjct: 366 SLFDPTIATFEDDAGAYDQKDAGGFIKLNALRMRIAANLKARKG 409 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: 514 Number of extensions: 17 Number of successful extensions: 4 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: 409 Length adjustment: 31 Effective length of query: 369 Effective length of database: 378 Effective search space: 139482 Effective search space used: 139482 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 Dsui_3248 Dsui_3248 (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.22810.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-145 468.9 0.0 9.4e-145 468.7 0.0 1.0 1 lcl|FitnessBrowser__PS:Dsui_3248 Dsui_3248 argininosuccinate synt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_3248 Dsui_3248 argininosuccinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 468.7 0.0 9.4e-145 9.4e-145 1 390 [. 6 402 .. 6 406 .. 0.96 Alignments for each domain: == domain 1 score: 468.7 bits; conditional E-value: 9.4e-145 TIGR00032 1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGae..kayviDareefvkdylfaaiq 74 kvvlaysGGlDtsv+lk+l++ +ev+++t+d+Gq+ e+l+ ++ kalk+G + + + D reefv+d++f+ + lcl|FitnessBrowser__PS:Dsui_3248 6 KVVLAYSGGLDTSVILKWLQDTyQCEVVTFTADLGQG-EELEPARTKALKFGIKpeNIFIDDLREEFVRDFVFPMFR 81 8*********************899***********9.9*************86314555579************** PP TIGR00032 75 anavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvreleli.Ree 150 an+vyeg+Yll+t++aRpliak+l+e+ + ga+a++hG+tgKGnDqvRFel ++l+p +kviaP+re++l Re+ lcl|FitnessBrowser__PS:Dsui_3248 82 ANTVYEGEYLLGTSIARPLIAKRLIEITNLTGADAISHGATGKGNDQVRFELGAYALKPGVKVIAPWREWDLLsREK 158 ***********************************************************************987*** PP TIGR00032 151 eieyaaekGievpveke...kaysiDenllgrsiEageLEdpsteppediyelvkdpiektedepevveieFekGvP 224 +++ya+++Gi+v+++++ ++ys+D nll++s+E+ +LE+p +e ed+++++++p++++ d +e++++eF +G lcl|FitnessBrowser__PS:Dsui_3248 159 LLAYAEQHGIPVEMKHKqggSPYSMDANLLHISYEGRHLENPAAEAEEDMWRWTVSPENAP-DAAEYLDLEFVQGDL 234 *************997634479*********************************998888.*************** PP TIGR00032 225 valngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLetlvltkdvlefkeive 301 va+ng+++++ el+ k+ne++gkhG+Gr+D vE+R++g+KsR++YE+p+ ++L++Ah+++e+ +l+++v+++k+ lcl|FitnessBrowser__PS:Dsui_3248 235 VAINGQNMKAHELLAKLNELGGKHGIGRLDLVENRYVGMKSRGCYETPGGTILLRAHRAIESITLDREVAHLKDDLM 311 ***************************************************************************** PP TIGR00032 302 ekyseliYkGlwfdplaealdalikktqervtGtvrvklfkGnaivigrk.seyslYdeelvsfek.dkefdqkdai 376 +y+ l+Y+G+w+ p+++al++li++tq+ v+Gtvr+kl+kGn+iv+gr+ +++sl+d+++++fe ++dqkda lcl|FitnessBrowser__PS:Dsui_3248 312 PRYASLVYNGYWWAPERKALQTLIDHTQQTVNGTVRLKLYKGNVIVVGRDsKTDSLFDPTIATFEDdAGAYDQKDAG 388 **************************************************8999***********944579****** PP TIGR00032 377 Gfikirglqikvyr 390 Gfik+++l++++ + lcl|FitnessBrowser__PS:Dsui_3248 389 GFIKLNALRMRIAA 402 ********998765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (409 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: 00:00:00.02 # Mc/sec: 7.54 // [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