Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate AZOBR_RS00785 AZOBR_RS00785 argininosuccinate synthase
Query= SwissProt::P59846 (400 letters) >FitnessBrowser__azobra:AZOBR_RS00785 Length = 411 Score = 513 bits (1322), Expect = e-150 Identities = 256/395 (64%), Positives = 305/395 (77%), Gaps = 4/395 (1%) Query: 2 KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIAL-- 59 K+VLAYSGGLDTS+ILKWL+ETY+ EV+ FTAD+GQGEE+E AR+KA G Sbjct: 11 KVVLAYSGGLDTSVILKWLQETYQCEVVTFTADLGQGEELEPARKKAELLGIKPENIFID 70 Query: 60 DLKEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKG 119 DL+EEFVRDFVFPM RA +YEG YLLGTSIARPLIAK + IA + GA+A+AHGATGKG Sbjct: 71 DLREEFVRDFVFPMFRANTLYEGTYLLGTSIARPLIAKRQIEIANQVGADAVAHGATGKG 130 Query: 120 NDQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQ--EKPYSMDAN 177 NDQVRFEL YAL+PDIK+IAPWREW R +I YAE + IP+ + E PYS DAN Sbjct: 131 NDQVRFELGYYALRPDIKIIAPWREWDLSSRTRLIDYAEKNQIPIAKDKRGEAPYSTDAN 190 Query: 178 LLHISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAA 237 LLHISYEG LEDPW EP + M+ + PE+APD P YVEVEF GD VA++G+ LSPAA Sbjct: 191 LLHISYEGKALEDPWVEPFEDMYTRSVAPEKAPDTPTYVEVEFKRGDAVAIDGKALSPAA 250 Query: 238 LLQRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQ 297 LL LN +GG +G+GR+D+VENR+VGMKSRGVYETPGGTIL A RA+ES+TLDR H Sbjct: 251 LLTELNRLGGENGIGRLDLVENRYVGMKSRGVYETPGGTILLAAHRAMESITLDRGAGHL 310 Query: 298 RDMLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSL 357 +D L P+YAEL+Y G+W++PER ALQA D V GV RLKL+KGNV VVGRK+P SL Sbjct: 311 KDELMPRYAELIYCGYWFSPERLALQALIDQTQEPVNGVVRLKLFKGNVTVVGRKSPNSL 370 Query: 358 YRQDLVSFDEAGGYDQKDAEGFIKIQALRLRVRAL 392 YR D V+F+E Y+QKDAEGFIK+ ALRLR+ A+ Sbjct: 371 YRMDYVTFEEDSVYNQKDAEGFIKLNALRLRLGAM 405 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: 507 Number of extensions: 11 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 400 Length of database: 411 Length adjustment: 31 Effective length of query: 369 Effective length of database: 380 Effective search space: 140220 Effective search space used: 140220 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 AZOBR_RS00785 AZOBR_RS00785 (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.27325.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-145 471.9 0.0 1.2e-145 471.7 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS00785 AZOBR_RS00785 argininosuccinate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS00785 AZOBR_RS00785 argininosuccinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 471.7 0.0 1.2e-145 1.2e-145 1 387 [. 11 401 .. 11 407 .. 0.97 Alignments for each domain: == domain 1 score: 471.7 bits; conditional E-value: 1.2e-145 TIGR00032 1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGae..kayviDareefvk 66 kvvlaysGGlDtsv+lk+l+e +ev+++t+d+Gq+ e+l+ +++ka lG + + + D reefv+ lcl|FitnessBrowser__azobra:AZOBR_RS00785 11 KVVLAYSGGLDTSVILKWLQETyQCEVVTFTADLGQG-EELEPARKKAELLGIKpeNIFIDDLREEFVR 78 8*********************899***********9.9************986214555589****** PP TIGR00032 67 dylfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdl 135 d++f+ +an++yeg+Yll+t++aRpliak+++e+a++ ga+avahG+tgKGnDqvRFel ++l+pd+ lcl|FitnessBrowser__azobra:AZOBR_RS00785 79 DFVFPMFRANTLYEGTYLLGTSIARPLIAKRQIEIANQVGADAVAHGATGKGNDQVRFELGYYALRPDI 147 ********************************************************************* PP TIGR00032 136 kviaPvreleli.ReeeieyaaekGievpvek..ekaysiDenllgrsiEageLEdpsteppediyelv 201 k+iaP+re++l+ R+ +i+ya+++ i+++ +k e +ys+D nll++s+E++ LEdp++ep ed+y+ lcl|FitnessBrowser__azobra:AZOBR_RS00785 148 KIIAPWREWDLSsRTRLIDYAEKNQIPIAKDKrgEAPYSTDANLLHISYEGKALEDPWVEPFEDMYTRS 216 ***********99***************99875579********************************9 PP TIGR00032 202 kdpiektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYE 270 + p++++ d+p +ve+eF++G va++g+ l+p l+ ++n+++g++G+Gr+D vE+R++g+KsR++YE lcl|FitnessBrowser__azobra:AZOBR_RS00785 217 VAPEKAP-DTPTYVEVEFKRGDAVAIDGKALSPAALLTELNRLGGENGIGRLDLVENRYVGMKSRGVYE 284 9777776.************************************************************* PP TIGR00032 271 apalllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvk 339 +p+ ++L+ Ah+++e+ +l++ ++k+ +y+eliY G+wf+p++ al+ali++tqe v+G+vr+k lcl|FitnessBrowser__azobra:AZOBR_RS00785 285 TPGGTILLAAHRAMESITLDRGAGHLKDELMPRYAELIYCGYWFSPERLALQALIDQTQEPVNGVVRLK 353 ********************************************************************* PP TIGR00032 340 lfkGnaivigrkseyslYdeelvsfekdkefdqkdaiGfikirglqik 387 lfkGn++v+grks++slY + v+fe+d+ ++qkda+Gfik+++l+ + lcl|FitnessBrowser__azobra:AZOBR_RS00785 354 LFKGNVTVVGRKSPNSLYRMDYVTFEEDSVYNQKDAEGFIKLNALRLR 401 ********************************************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (411 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: 7.56 // [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