Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate AO353_05630 AO353_05630 carbamoyl phosphate synthase large subunit
Query= BRENDA::P00968 (1073 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05630 Length = 1073 Score = 1598 bits (4139), Expect = 0.0 Identities = 805/1073 (75%), Positives = 916/1073 (85%), Gaps = 1/1073 (0%) Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDP M Sbjct: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPAM 60 Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120 ADATYIEPI W+ V KIIEKERPDA+LPTMGGQTALNCAL+LER+G+LE+FGV MIGA A Sbjct: 61 ADATYIEPIKWQTVAKIIEKERPDALLPTMGGQTALNCALDLEREGILEKFGVEMIGANA 120 Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180 D IDKAEDR RFD AMK IGL RSGIAH+MEEA AV +GFPCIIRPSFTMGG+GGG Sbjct: 121 DTIDKAEDRSRFDKAMKSIGLACPRSGIAHSMEEANAVLEKLGFPCIIRPSFTMGGTGGG 180 Query: 181 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDK DNCIIVCSIENFD M Sbjct: 181 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKKDNCIIVCSIENFDPM 240 Query: 241 GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300 G+HTGDSITVAPAQTLTDKEYQI+RNAS+AVLREIGVETGGSNVQF + P GR++VIEM Sbjct: 241 GVHTGDSITVAPAQTLTDKEYQILRNASLAVLREIGVETGGSNVQFGICPNTGRMVVIEM 300 Query: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEL NDITGG+TPASFEPSIDYVVTK+P Sbjct: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELSNDITGGKTPASFEPSIDYVVTKLP 360 Query: 361 RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420 RF FEKF A+ RLTTQMKSVGEVMAIGRT QESLQKALRGLEVG G D K+ L +PE+ Sbjct: 361 RFAFEKFPKADARLTTQMKSVGEVMAIGRTFQESLQKALRGLEVGVCGLDEKLDLSNPES 420 Query: 421 LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480 ++ ++REL GA+RIWY+ADA RAG+SV+ +F +T ID WFLVQ+E+L++ EEKV +G Sbjct: 421 MSVLKRELTVPGAERIWYVADAMRAGMSVEDIFGMTMIDPWFLVQMEDLIKDEEKVKTLG 480 Query: 481 ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540 +T ++ D + +LKRKGF+D RLAKL GV E +R R + ++ PVYKRVDTCAAEFATDT Sbjct: 481 LTSIDRDMMFRLKRKGFSDQRLAKLLGVTEKSLRAHRHKLEVFPVYKRVDTCAAEFATDT 540 Query: 541 AYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN 600 AY+YSTYEEECEA PS R+KIM+LGGGPNRIGQGIEFDYCCVHA+LALR+DGYETIMVN Sbjct: 541 AYLYSTYEEECEAAPS-GRDKIMILGGGPNRIGQGIEFDYCCVHAALALRDDGYETIMVN 599 Query: 601 CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 660 CNPETVSTDYDTSDRLYFEPVTLEDVLEIVR+EKPKGVIVQYGGQTPLKLARALEAAGVP Sbjct: 600 CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRVEKPKGVIVQYGGQTPLKLARALEAAGVP 659 Query: 661 VIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVL 720 +IGTSPDAIDRAEDRERFQ V+RL L+QP NATV + + A+ A +IGYPLVVRPSYVL Sbjct: 660 IIGTSPDAIDRAEDRERFQQMVQRLNLRQPPNATVRSEDEAIRAAAKIGYPLVVRPSYVL 719 Query: 721 GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME 780 GGRAMEIVY+E +L+RY + AV VSND+PVLLDHFL+ A+E+DVDA+CDG V+IG IM+ Sbjct: 720 GGRAMEIVYEEEELKRYLREAVQVSNDSPVLLDHFLNCAIEMDVDAVCDGTDVVIGAIMQ 779 Query: 781 HIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI 840 HIEQAGVHSGDSACSLP Y+L IQD MR+QV+K+A EL V GLMNVQ A++ ++Y+I Sbjct: 780 HIEQAGVHSGDSACSLPPYSLPLHIQDEMREQVKKMALELGVVGLMNVQLALQGEDIYVI 839 Query: 841 EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKF 900 EVNPRA+RTVPFVSK GV LA +AARVMAGK+L E G TKE+IP +YSVKE V PF KF Sbjct: 840 EVNPRASRTVPFVSKCIGVSLAMIAARVMAGKTLKEIGFTKEIIPNFYSVKEAVFPFAKF 899 Query: 901 PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDL 960 PGVDP+LGPEM+STGEVMGVG TF EAFAKAQ+G++ + G A +SVR+ DK V + Sbjct: 900 PGVDPILGPEMKSTGEVMGVGDTFGEAFAKAQMGASEVLPTGGTAFISVRDDDKPLVAGV 959 Query: 961 AAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGR 1020 A L+ GFE+ AT GTA ++ AG+ R VNKV EGRPH+ D IKN E T IINTT GR Sbjct: 960 ARDLINLGFEVVATAGTAKLIEAAGLKVRRVNKVTEGRPHVVDMIKNDEVTLIINTTEGR 1019 Query: 1021 RAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQIK 1073 ++I DS IRR+ALQ+K++ TT+ G A AL + V +Q++HA +K Sbjct: 1020 QSIADSYSIRRNALQHKIYCTTTIAAGEAICEALKFGPEKTVRRLQDLHAGLK 1072 Lambda K H 0.318 0.135 0.383 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: 3194 Number of extensions: 139 Number of successful extensions: 12 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: 1073 Length of database: 1073 Length adjustment: 45 Effective length of query: 1028 Effective length of database: 1028 Effective search space: 1056784 Effective search space used: 1056784 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 58 (26.9 bits)
Align candidate AO353_05630 AO353_05630 (carbamoyl phosphate synthase large subunit)
to HMM TIGR01369 (carB: carbamoyl-phosphate synthase, large subunit (EC 6.3.5.5))
# 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/TIGR01369.hmm # target sequence database: /tmp/gapView.14953.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01369 [M=1052] Accession: TIGR01369 Description: CPSaseII_lrg: carbamoyl-phosphate synthase, large subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1574.1 0.0 0 1573.9 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_05630 AO353_05630 carbamoyl phosphate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_05630 AO353_05630 carbamoyl phosphate synthase large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1573.9 0.0 0 0 1 1052 [] 2 1053 .. 2 1053 .. 0.98 Alignments for each domain: == domain 1 score: 1573.9 bits; conditional E-value: 0 TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkv 63 pkr+dik++l++G+GpivigqA+EFDYsG+qa+kal+eeg++v+Lvnsn+At+mtd+++ad++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_05630 2 PKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPAMADAT 64 689************************************************************ PP TIGR01369 64 YiePltveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkae 126 YieP+++++v+kiiekErpDa+l+t+GGqtaLn+a++le++G+Lek+gv+++G++ ++i+kae lcl|FitnessBrowser__pseudo3_N2E3:AO353_05630 65 YIEPIKWQTVAKIIEKERPDALLPTMGGQTALNCALDLEREGILEKFGVEMIGANADTIDKAE 127 *************************************************************** PP TIGR01369 127 dRekFkealkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelke 189 dR +F++a+k i++ ++s i++s+eea ++ e++g+P+i+R++ft+gGtG+gia+n+ee++e lcl|FitnessBrowser__pseudo3_N2E3:AO353_05630 128 DRSRFDKAMKSIGLACPRSGIAHSMEEANAVLEKLGFPCIIRPSFTMGGTGGGIAYNREEFEE 190 *************************************************************** PP TIGR01369 190 lvekalkaspikqvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPs 252 +++++l++sp+k++l+++sl gwkE+E+EvvRD+kdnciivc+iEn+Dp+GvHtGdsi+vaP+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_05630 191 ICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKKDNCIIVCSIENFDPMGVHTGDSITVAPA 253 *************************************************************** PP TIGR01369 253 qtLtdkeyqllRdaslkiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtG 314 qtLtdkeyq+lR+asl+++re+gve++ +nvqf++ P++ r+vviE+npRvsRssALAskAtG lcl|FitnessBrowser__pseudo3_N2E3:AO353_05630 254 QTLTDKEYQILRNASLAVLREIGVETGgSNVQFGICPNTGRMVVIEMNPRVSRSSALASKATG 316 *************************988*********************************** PP TIGR01369 315 yPiAkvaaklavGysLdelkndvtk.etvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmk 376 +PiAkvaaklavGy+Ldel+nd+t+ +t+AsfEPs+DYvv+k+Pr++++kf k+d +l+tqmk lcl|FitnessBrowser__pseudo3_N2E3:AO353_05630 317 FPIAKVAAKLAVGYTLDELSNDITGgKTPASFEPSIDYVVTKLPRFAFEKFPKADARLTTQMK 379 ************************879************************************ PP TIGR01369 377 svGEvmaigrtfeealqkalrsleekllglklkeke..aesdeeleealkkpndrRlfaiaea 437 svGEvmaigrtf+e+lqkalr le ++ gl++k + es + l+++l+ p ++R++++a+a lcl|FitnessBrowser__pseudo3_N2E3:AO353_05630 380 SVGEVMAIGRTFQESLQKALRGLEVGVCGLDEKLDLsnPESMSVLKRELTVPGAERIWYVADA 442 *****************************887755400455667899**************** PP TIGR01369 438 lrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGfsdeqiakl 500 +r+g+sve+++ +t id +fl ++++l++ e+++++ l+ ++++++ ++k++Gfsd+++akl lcl|FitnessBrowser__pseudo3_N2E3:AO353_05630 443 MRAGMSVEDIFGMTMIDPWFLVQMEDLIKDEEKVKTLGLTSIDRDMMFRLKRKGFSDQRLAKL 505 *************************************************************** PP TIGR01369 501 vkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeeekddvevtekkkvlvlGsG 563 ++v+e+++r+ r++l++ pv+krvDt+aaEf ++t+YlYstyeee++ +++ ++ k+++lG+G lcl|FitnessBrowser__pseudo3_N2E3:AO353_05630 506 LGVTEKSLRAHRHKLEVFPVYKRVDTCAAEFATDTAYLYSTYEEECEAAPSGRD-KIMILGGG 567 *********************************************766666665.******** PP TIGR01369 564 piRigqgvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiie 626 p+Rigqg+EFDyc+vha+lalr+ gy+ti++n+nPEtvstDyd++drLyFe++t+edvl+i++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_05630 568 PNRIGQGIEFDYCCVHAALALRDDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVR 630 *************************************************************** PP TIGR01369 627 kekvegvivqlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgke 689 ek++gvivq+gGqt+l+la++le+agv+i+Gts+++idraEdRe+F++++++l++ qp +++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_05630 631 VEKPKGVIVQYGGQTPLKLARALEAAGVPIIGTSPDAIDRAEDRERFQQMVQRLNLRQPPNAT 693 *************************************************************** PP TIGR01369 690 atsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeavevskekPvlidkyle 752 ++s +ea ++a++igyP++vRpsyvlgGrameiv++eeel+ryl+eav+vs+++Pvl+d++l+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_05630 694 VRSEDEAIRAAAKIGYPLVVRPSYVLGGRAMEIVYEEEELKRYLREAVQVSNDSPVLLDHFLN 756 *************************************************************** PP TIGR01369 753 davEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakel 815 a+E+dvDav+dg++v+i +i++HiE+aGvHsGDs+++lpp +l +++++++e+vkk+a el lcl|FitnessBrowser__pseudo3_N2E3:AO353_05630 757 CAIEMDVDAVCDGTDVVIGAIMQHIEQAGVHSGDSACSLPPYSLPLHIQDEMREQVKKMALEL 819 *************************************************************** PP TIGR01369 816 kvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkk 878 v+Gl+n+q+++++e++yviEvn+RasRtvPfvsk +gv+l+ +a++v++gk+l+e g +k lcl|FitnessBrowser__pseudo3_N2E3:AO353_05630 820 GVVGLMNVQLALQGEDIYVIEVNPRASRTVPFVSKCIGVSLAMIAARVMAGKTLKE--IGFTK 880 ********************************************************..6789* PP TIGR01369 879 ekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgs 941 e +++++vk+avf+f+k+ gvd++lgpemkstGEvmg+g+++ ea++ka++ +++++++ g+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_05630 881 EIIPNFYSVKEAVFPFAKFPGVDPILGPEMKSTGEVMGVGDTFGEAFAKAQMGASEVLPTGGT 943 *************************************************************** PP TIGR01369 942 vllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlkvseeaekilellke 1004 +++sv+d dk + +a+ l ++g++v+at+gtak +e ag k++ v+kv+e ++++++++k+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_05630 944 AFISVRDDDKPLVAGVARDLINLGFEVVATAGTAKLIEAAGLKVRRVNKVTEGRPHVVDMIKN 1006 *************************************************************** PP TIGR01369 1005 eeielvinltskkkkaaekgykirreaveykvplvteletaealleal 1052 +e++l+in+t+ ++++ ++y+irr+a+++k+ + t++++ ea++eal lcl|FitnessBrowser__pseudo3_N2E3:AO353_05630 1007 DEVTLIINTTE-GRQSIADSYSIRRNALQHKIYCTTTIAAGEAICEAL 1053 ********997.77788899***********************99986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1052 nodes) Target sequences: 1 (1073 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: 0.08u 0.04s 00:00:00.12 Elapsed: 00:00:00.12 # Mc/sec: 8.92 // [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