Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate GFF2423 HP15_2367 argininosuccinate synthase
Query= SwissProt::P59846 (400 letters) >FitnessBrowser__Marino:GFF2423 Length = 408 Score = 504 bits (1299), Expect = e-147 Identities = 246/392 (62%), Positives = 304/392 (77%), Gaps = 2/392 (0%) Query: 2 KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIALDL 61 K+VLAYSGGLDTS+I++WL++TY EV+ FTADIGQGEEVE AR KA G + DL Sbjct: 11 KVVLAYSGGLDTSVIVRWLQDTYNCEVVTFTADIGQGEEVEPARAKAEALGVKEIYIEDL 70 Query: 62 KEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGND 121 +EEFVRD+VFPM RA +YEG YLLGTSIARPLIAK L+ IA E GA+AI+HGATGKGND Sbjct: 71 REEFVRDYVFPMFRANTIYEGEYLLGTSIARPLIAKRLIDIANETGADAISHGATGKGND 130 Query: 122 QVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEK-PYSMDANLLH 180 QVRFEL AYALKP +KVIAPWREW R++++ Y E IPV + + K PYSMDANLLH Sbjct: 131 QVRFELGAYALKPGVKVIAPWREWDLNSREKLLKYCEERNIPVEMKKGKSPYSMDANLLH 190 Query: 181 ISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALLQ 240 ISYEG LEDPWAE + M+R + PE APD P YVE+ + +GD VA++G+ + P +L+ Sbjct: 191 ISYEGINLEDPWAEAEEDMWRWSVSPEAAPDEPTYVELTYKKGDIVAIDGQDMKPHLVLE 250 Query: 241 RLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRDM 300 LN++ G +G+GR+DIVENR+VGMKSRG YETPGGTI+ A RA+ES+TLDREV H +D Sbjct: 251 TLNKLAGANGIGRLDIVENRYVGMKSRGCYETPGGTIMLRAHRAIESITLDREVAHLKDS 310 Query: 301 LSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYRQ 360 + P+YAE++Y G+W++PEREALQA D V G RLKLYKGNV VVGRK+ SL+ + Sbjct: 311 IMPRYAEVIYNGYWWSPEREALQALIDQTQNYVNGTVRLKLYKGNVDVVGRKSEDSLFDE 370 Query: 361 DLVSFDE-AGGYDQKDAEGFIKIQALRLRVRA 391 + +F+E G YDQKDAEGFIK+ ALRLR+ A Sbjct: 371 KIATFEEDQGAYDQKDAEGFIKLNALRLRIAA 402 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: 517 Number of extensions: 14 Number of successful extensions: 3 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: 408 Length adjustment: 31 Effective length of query: 369 Effective length of database: 377 Effective search space: 139113 Effective search space used: 139113 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 GFF2423 HP15_2367 (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.17439.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-146 473.6 0.0 3.7e-146 473.4 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF2423 HP15_2367 argininosuccinate synt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF2423 HP15_2367 argininosuccinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 473.4 0.0 3.7e-146 3.7e-146 1 389 [. 11 401 .. 11 406 .. 0.98 Alignments for each domain: == domain 1 score: 473.4 bits; conditional E-value: 3.7e-146 TIGR00032 1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdylfaaiq 74 kvvlaysGGlDtsv++++l++ ++ev+++t+d+Gq+ e+++ ++ ka +lG+++ y+ D reefv+dy+f+ + lcl|FitnessBrowser__Marino:GFF2423 11 KVVLAYSGGLDTSVIVRWLQDTyNCEVVTFTADIGQG-EEVEPARAKAEALGVKEIYIEDLREEFVRDYVFPMFR 84 8*********************99************9.9************************************ PP TIGR00032 75 anavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvreleli.R 148 an++yeg+Yll+t++aRpliak+l+++a++ ga+a++hG+tgKGnDqvRFel ++l+p +kviaP+re++l R lcl|FitnessBrowser__Marino:GFF2423 85 ANTIYEGEYLLGTSIARPLIAKRLIDIANETGADAISHGATGKGNDQVRFELGAYALKPGVKVIAPWREWDLNsR 159 ************************************************************************88* PP TIGR00032 149 eeeieyaaekGievpvekek.aysiDenllgrsiEageLEdpsteppediyelvkdpiektedepevveieFekG 222 e++++y +e+ i+v+++k k +ys+D nll++s+E+ +LEdp++e ed++++ ++p++++ dep +ve++++kG lcl|FitnessBrowser__Marino:GFF2423 160 EKLLKYCEERNIPVEMKKGKsPYSMDANLLHISYEGINLEDPWAEAEEDMWRWSVSPEAAP-DEPTYVELTYKKG 233 ****************996439*********************************888887.************* PP TIGR00032 223 vPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLetlvltkdvlefk 297 va++g+ ++p +++++n++ag++G+Gr+DivE+R++g+KsR++YE+p+ +++++Ah+++e+ +l+++v+++k lcl|FitnessBrowser__Marino:GFF2423 234 DIVAIDGQDMKPHLVLETLNKLAGANGIGRLDIVENRYVGMKSRGCYETPGGTIMLRAHRAIESITLDREVAHLK 308 *************************************************************************** PP TIGR00032 298 eiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkGnaivigrkseyslYdeelvsfek.dkefd 371 + + +y+e+iY+G+w++p++eal+ali++tq+ v+Gtvr+kl+kGn+ v+grkse+sl+de++++fe+ + ++d lcl|FitnessBrowser__Marino:GFF2423 309 DSIMPRYAEVIYNGYWWSPEREALQALIDQTQNYVNGTVRLKLYKGNVDVVGRKSEDSLFDEKIATFEEdQGAYD 383 ********************************************************************955689* PP TIGR00032 372 qkdaiGfikirglqikvy 389 qkda+Gfik+++l+ ++ lcl|FitnessBrowser__Marino:GFF2423 384 QKDAEGFIKLNALRLRIA 401 *************98876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (408 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: 7.39 // [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