Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate SMc03826 SMc03826 argininosuccinate synthase
Query= SwissProt::P59846 (400 letters) >FitnessBrowser__Smeli:SMc03826 Length = 405 Score = 494 bits (1272), Expect = e-144 Identities = 251/397 (63%), Positives = 301/397 (75%), Gaps = 3/397 (0%) Query: 2 KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIALDL 61 K+VLAYSGGLDTSIILKWL+ AEV+ FTAD+GQGEE+E AR+KA G + D+ Sbjct: 9 KVVLAYSGGLDTSIILKWLQTELGAEVVTFTADLGQGEELEPARKKAEMLGIKEIYIEDV 68 Query: 62 KEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGND 121 +EEFVRDFVFPM RA AVYEG YLLGTSIARPLI+KHL+ IA + GA+AIAHGATGKGND Sbjct: 69 REEFVRDFVFPMFRANAVYEGVYLLGTSIARPLISKHLIDIARKTGADAIAHGATGKGND 128 Query: 122 QVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQ--EKPYSMDANLL 179 QVRFEL+AYAL PDIK+IAPWR+WSF+ R +++ +AE H IPV + E P+S+DANLL Sbjct: 129 QVRFELSAYALNPDIKIIAPWRDWSFKSRTDLLEFAEKHQIPVAKDKKGEAPFSVDANLL 188 Query: 180 HISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALL 239 H S EG VLEDP E P+ + T PE APD ++V F GD V+++G R+SPA LL Sbjct: 189 HSSSEGKVLEDPAREAPEYVHMRTISPEAAPDKATVIKVGFERGDAVSIDGVRMSPATLL 248 Query: 240 QRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRD 299 +LNE G +G+GR+D+VENRFVGMKSRGVYETPGGTIL A RA+ES+TLDR H +D Sbjct: 249 AKLNEYGRDNGIGRLDLVENRFVGMKSRGVYETPGGTILLAAHRAIESITLDRGAAHLKD 308 Query: 300 MLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYR 359 L P+YAEL+YYGFW++PERE LQA D V G LKLYKGNV V+GR++ KSLY Sbjct: 309 ELMPRYAELIYYGFWFSPEREMLQAAIDRSQEHVEGEVTLKLYKGNVMVIGRESGKSLYS 368 Query: 360 QDLVSF-DEAGGYDQKDAEGFIKIQALRLRVRALVER 395 LV+F D+ G YDQKDA GFIK+ ALRLR A R Sbjct: 369 DKLVTFEDDQGAYDQKDAAGFIKLNALRLRTLAARNR 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: 512 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: 405 Length adjustment: 31 Effective length of query: 369 Effective length of database: 374 Effective search space: 138006 Effective search space used: 138006 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 SMc03826 SMc03826 (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.17904.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-145 469.8 0.0 5e-145 469.6 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SMc03826 SMc03826 argininosuccinate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc03826 SMc03826 argininosuccinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 469.6 0.0 5e-145 5e-145 1 390 [. 9 401 .. 9 405 .] 0.97 Alignments for each domain: == domain 1 score: 469.6 bits; conditional E-value: 5e-145 TIGR00032 1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdylfaaiq 74 kvvlaysGGlDts++lk+l+ + gaev+++t+d+Gq+ e+l+ +++ka lG ++ y+ D reefv+d++f+ + lcl|FitnessBrowser__Smeli:SMc03826 9 KVVLAYSGGLDTSIILKWLQTElGAEVVTFTADLGQG-EELEPARKKAEMLGIKEIYIEDVREEFVRDFVFPMFR 82 8***********************************9.9************************************ PP TIGR00032 75 anavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvreleli.R 148 anavyeg+Yll+t++aRpli+k l+++a+k ga+a+ahG+tgKGnDqvRFels ++lnpd+k+iaP+r++ + R lcl|FitnessBrowser__Smeli:SMc03826 83 ANAVYEGVYLLGTSIARPLISKHLIDIARKTGADAIAHGATGKGNDQVRFELSAYALNPDIKIIAPWRDWSFKsR 157 ************************************************************************88* PP TIGR00032 149 eeeieyaaekGievpvek..ekaysiDenllgrsiEageLEdpsteppediyelvkdpiektedepevveieFek 221 ++++e+a+++ i+v+ +k e ++s+D nll+ s E++ LEdp e pe +++ + +p++++ d++ v++++Fe+ lcl|FitnessBrowser__Smeli:SMc03826 158 TDLLEFAEKHQIPVAKDKkgEAPFSVDANLLHSSSEGKVLEDPAREAPEYVHMRTISPEAAP-DKATVIKVGFER 231 **************988744689*********************************888877.************ PP TIGR00032 222 GvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLetlvltkdvlef 296 G v+++g++++p +l+ k+ne ++ +G+Gr+D vE+R +g+KsR++YE+p+ ++L+ Ah+++e+ +l++ +++ lcl|FitnessBrowser__Smeli:SMc03826 232 GDAVSIDGVRMSPATLLAKLNEYGRDNGIGRLDLVENRFVGMKSRGVYETPGGTILLAAHRAIESITLDRGAAHL 306 *************************************************************************** PP TIGR00032 297 keiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkGnaivigrkseyslYdeelvsfek.dkef 370 k+ +y+eliY+G+wf+p++e+l+a+i+++qe+v G+v++kl+kGn++vigr+s +slY+++lv+fe + ++ lcl|FitnessBrowser__Smeli:SMc03826 307 KDELMPRYAELIYYGFWFSPEREMLQAAIDRSQEHVEGEVTLKLYKGNVMVIGRESGKSLYSDKLVTFEDdQGAY 381 *********************************************************************955689 PP TIGR00032 371 dqkdaiGfikirglqikvyr 390 dqkda+Gfik+++l+ ++ + lcl|FitnessBrowser__Smeli:SMc03826 382 DQKDAAGFIKLNALRLRTLA 401 **************988765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (405 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.82 // [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