Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate AMB_RS03605 AMB_RS03605 carbamoyl-phosphate synthase large subunit
Query= BRENDA::P00968 (1073 letters) >FitnessBrowser__Magneto:AMB_RS03605 Length = 1085 Score = 1293 bits (3347), Expect = 0.0 Identities = 672/1071 (62%), Positives = 820/1071 (76%), Gaps = 20/1071 (1%) Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60 MPKRTDIKSILI+GAGPIVIGQACEFDYSG QACKAL++EGYRVILVNSNPATIMTDP + Sbjct: 1 MPKRTDIKSILIIGAGPIVIGQACEFDYSGVQACKALKDEGYRVILVNSNPATIMTDPGL 60 Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120 ADATYIEPI E+V KIIEKERPDA+LPTMGGQTALN A++L G+LE+FGV MI A Sbjct: 61 ADATYIEPITPEIVAKIIEKERPDALLPTMGGQTALNTAMKLADMGILEKFGVEMIAAKR 120 Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180 D I KAEDR F AM KIGLE+ +S + T++EA VG P IIRPSFT+ G+GGG Sbjct: 121 DVIAKAEDRLLFRDAMDKIGLESPKSRMVKTLQEAREALDFVGLPAIIRPSFTLAGTGGG 180 Query: 181 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240 IAYN E+E I + GL SP E+L++ES++GWKEYEMEVVRDK DNCII+CSIEN D M Sbjct: 181 IAYNVAEYEHIVSGGLAASPVHEVLVEESVLGWKEYEMEVVRDKKDNCIIICSIENVDPM 240 Query: 241 GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300 G+HTGDSITVAPA TLTDKEYQIMRNAS+AVLREIGV+TGGSNVQFAVNPK+GR+ VIEM Sbjct: 241 GVHTGDSITVAPALTLTDKEYQIMRNASLAVLREIGVDTGGSNVQFAVNPKDGRMTVIEM 300 Query: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEL NDIT G TPASFEP+IDYVVTKIP Sbjct: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELTNDIT-GCTPASFEPTIDYVVTKIP 359 Query: 361 RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFD----PKVSLD 416 RF FEKF GA+ LTT MKSVGE MAIGRT QESLQK LR +E G TG D P Sbjct: 360 RFTFEKFPGADPNLTTSMKSVGEAMAIGRTFQESLQKGLRSMETGLTGLDEVEIPGAGAG 419 Query: 417 DPEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKV 476 D + ++ L DR+ IA AFR GL++D V D+WFL Q++ +V E ++ Sbjct: 420 DMK--DAVKSALAQPRHDRLLVIAQAFRFGLTIDEVHAACFYDKWFLAQLKGIVDAEAEI 477 Query: 477 AEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEF 536 G+ ++A L +LK+ GF+D RLAKL+G E R+ ++ PV+KR+DTCAAEF Sbjct: 478 RAKGLP-IDAPGLLRLKKMGFSDQRLAKLSGKSLVETAFRREVLNVKPVFKRIDTCAAEF 536 Query: 537 ATDTAYMYSTYE------EECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALR 590 + TAYMYS YE ECE++PS DR+K+++LGGGPNRIGQGIEFDYCCVHA+ AL Sbjct: 537 PSSTAYMYSCYEGDGVNPPECESDPS-DRDKVIILGGGPNRIGQGIEFDYCCVHAAYALD 595 Query: 591 EDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIE----KPKGVIVQYGGQT 646 E G ETIMVNCNPETVSTDYDTSDRLYFEP+T E V+++VR E K G IVQ+GGQT Sbjct: 596 EAGKETIMVNCNPETVSTDYDTSDRLYFEPLTAETVIDLVRKEQSNGKVLGCIVQFGGQT 655 Query: 647 PLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAK 706 PLKLA ALE AG+P++GTSPD+ID AEDRERFQ + +L LKQPAN T ++E A++ A+ Sbjct: 656 PLKLAHALEQAGIPILGTSPDSIDLAEDRERFQKMLHQLGLKQPANGTARSLEEAIKVAE 715 Query: 707 EIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDA 766 +IGYP+V+RPS+VLGGRAM+IVYD L RY AV VS D PVL+D++L DA+EVDVDA Sbjct: 716 KIGYPVVIRPSFVLGGRAMQIVYDHEALERYMVEAVKVSGDDPVLIDYYLKDAIEVDVDA 775 Query: 767 ICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLM 826 +CDG V + GIM+HIE+AG+HSGDSACSLP Y+L + + +Q +A L V GLM Sbjct: 776 LCDGNQVYVAGIMQHIEEAGIHSGDSACSLPPYSLDKATIAELERQTAAMAKALNVVGLM 835 Query: 827 NVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPP 886 N Q+A+K+ ++Y++EVNPRA+RTVPFV+KATGVP+AK+AARVMAG++LA G++ Sbjct: 836 NCQYAIKDGDIYILEVNPRASRTVPFVAKATGVPIAKIAARVMAGETLASFGLSTRPELK 895 Query: 887 YYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRAL 946 + +VKE V PF +FPGVD LLGPEM+STGEVMG+ FA AFAK+QLG+ + + G A Sbjct: 896 HVAVKEAVFPFARFPGVDILLGPEMKSTGEVMGIDSDFARAFAKSQLGAGTNLPTEGGAF 955 Query: 947 LSVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGI-NPRLVNKVHEGRPHIQDRI 1005 +SVR+GDK +V++A +LL+ GF++ AT GTA L + G+ +VNKV EGRPH D + Sbjct: 956 ISVRDGDKPAMVEIARRLLEMGFKVMATDGTAFYLKDRGVTGVTIVNKVLEGRPHCVDAM 1015 Query: 1006 KNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNA 1056 NG+ ++NTT G +A++DS IRR+AL + + TT+ G A A+ A Sbjct: 1016 MNGQVQLVVNTTEGSQAVKDSFSIRRTALTNNIPHYTTVAGARAAVEAIEA 1066 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: 3035 Number of extensions: 123 Number of successful extensions: 18 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: 1085 Length adjustment: 46 Effective length of query: 1027 Effective length of database: 1039 Effective search space: 1067053 Effective search space used: 1067053 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 AMB_RS03605 AMB_RS03605 (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.36406.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 1506.3 0.0 0 1506.1 0.0 1.0 1 FitnessBrowser__Magneto:AMB_RS03605 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Magneto:AMB_RS03605 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1506.1 0.0 0 0 1 1051 [. 2 1063 .. 2 1064 .. 0.97 Alignments for each domain: == domain 1 score: 1506.1 bits; conditional E-value: 0 TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltvea 72 pkr+dik++l+iG+GpivigqA+EFDYsG qa+kalk+eg++v+Lvnsn+At+mtd+ lad++YieP+t+e+ FitnessBrowser__Magneto:AMB_RS03605 2 PKRTDIKSILIIGAGPIVIGQACEFDYSGVQACKALKDEGYRVILVNSNPATIMTDPGLADATYIEPITPEI 73 689********************************************************************* PP TIGR01369 73 vekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevak 144 v+kiiekErpDa+l+t+GGqtaLn a++l ++G+Lek+gv+++ +k ++i+kaedR +F++a+++i++e +k FitnessBrowser__Magneto:AMB_RS03605 74 VAKIIEKERPDALLPTMGGQTALNTAMKLADMGILEKFGVEMIAAKRDVIAKAEDRLLFRDAMDKIGLESPK 145 ************************************************************************ PP TIGR01369 145 seivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwkEiE 216 s++v++ +ea ea + +g+P i+R++ftl+GtG+gia+n +e +++v+ +l+asp+++vlve+s+ gwkE+E FitnessBrowser__Magneto:AMB_RS03605 146 SRMVKTLQEAREALDFVGLPAIIRPSFTLAGTGGGIAYNVAEYEHIVSGGLAASPVHEVLVEESVLGWKEYE 217 ************************************************************************ PP TIGR01369 217 yEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvqfald 287 +EvvRD+kdncii+c+iEn+Dp+GvHtGdsi+vaP+ tLtdkeyq++R+asl+++re+gv+++ +nvqfa++ FitnessBrowser__Magneto:AMB_RS03605 218 MEVVRDKKDNCIIICSIENVDPMGVHTGDSITVAPALTLTDKEYQIMRNASLAVLREIGVDTGgSNVQFAVN 289 ************************************************************9988******** PP TIGR01369 288 PeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtketvAsfEPslDYvvvkiPrw 359 P++ r++viE+npRvsRssALAskAtG+PiAkvaaklavGy+Ldel+nd+t+ t+AsfEP++DYvv+kiPr+ FitnessBrowser__Magneto:AMB_RS03605 290 PKDGRMTVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELTNDITGCTPASFEPTIDYVVTKIPRF 361 ************************************************************************ PP TIGR01369 360 dldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllg...lklkek.eaesdeeleealkkpn 427 ++kf ++d +l+t+mksvGE maigrtf+e+lqk+lrs+e++l+g ++++ + + +++++++al +p FitnessBrowser__Magneto:AMB_RS03605 362 TFEKFPGADPNLTTSMKSVGEAMAIGRTFQESLQKGLRSMETGLTGldeVEIPGAgAGDMKDAVKSALAQPR 433 **********************************************4443444441445667788999**** PP TIGR01369 428 drRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGfsdeqiak 499 ++Rl++ia+a+r g++++ev+ ++ +d++fl +lk +v++e e++ + l +++ l ++kk+Gfsd+++ak FitnessBrowser__Magneto:AMB_RS03605 434 HDRLLVIAQAFRFGLTIDEVHAACFYDKWFLAQLKGIVDAEAEIRAKGLP-IDAPGLLRLKKMGFSDQRLAK 504 ********************************************966655.9******************** PP TIGR01369 500 lvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeee.....kddvevtekkkvlvlGsGpiR 566 l ++s e r+ l++ pv+kr+Dt+aaEf+++t+Y+Ys ye++ + +++ ++++kv++lG+Gp+R FitnessBrowser__Magneto:AMB_RS03605 505 LSGKSLVETAFRREVLNVKPVFKRIDTCAAEFPSSTAYMYSCYEGDgvnppECESDPSDRDKVIILGGGPNR 576 ********************************************99777766677788889*********** PP TIGR01369 567 igqgvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiiekekve....gvi 634 igqg+EFDyc+vha+ al eag++ti++n+nPEtvstDyd++drLyFe+lt e+v+d+++ke+ + g+i FitnessBrowser__Magneto:AMB_RS03605 577 IGQGIEFDYCCVHAAYALDEAGKETIMVNCNPETVSTDYDTSDRLYFEPLTAETVIDLVRKEQSNgkvlGCI 648 **************************************************************866223379* PP TIGR01369 635 vqlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyP 706 vq+gGqt+l+la++le+ag++ilGts++sid aEdRe+F+k+l++lg+kqp++ +a+s+eea ++a++igyP FitnessBrowser__Magneto:AMB_RS03605 649 VQFGGQTPLKLAHALEQAGIPILGTSPDSIDLAEDRERFQKMLHQLGLKQPANGTARSLEEAIKVAEKIGYP 720 ************************************************************************ PP TIGR01369 707 vlvRpsyvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiE 778 v++Rps+vlgGram+iv+++e lery+ eav+vs + Pvlid yl+da+EvdvDa++dg++v++agi++HiE FitnessBrowser__Magneto:AMB_RS03605 721 VVIRPSFVLGGRAMQIVYDHEALERYMVEAVKVSGDDPVLIDYYLKDAIEVDVDALCDGNQVYVAGIMQHIE 792 ************************************************************************ PP TIGR01369 779 eaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvsk 850 eaG+HsGDs+++lpp +l++ + +++++++++ak+l+v+Gl+n q+++kd+++y++Evn+RasRtvPfv+k FitnessBrowser__Magneto:AMB_RS03605 793 EAGIHSGDSACSLPPYSLDKATIAELERQTAAMAKALNVVGLMNCQYAIKDGDIYILEVNPRASRTVPFVAK 864 ************************************************************************ PP TIGR01369 851 algvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdle 922 a+gvp++k+a++v++g++l++ g++++++ k+vavk+avf+f+++ gvd++lgpemkstGEvmgi++d++ FitnessBrowser__Magneto:AMB_RS03605 865 ATGVPIAKIAARVMAGETLAS--FGLSTRPELKHVAVKEAVFPFARFPGVDILLGPEMKSTGEVMGIDSDFA 934 *********************..56799******************************************** PP TIGR01369 923 eallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagik.aevvlkvse 993 +a++k++l ++++++++g +++sv+d dk +++e+a++l e+g+kv+at+gta +l+++g++ ++ v+kv e FitnessBrowser__Magneto:AMB_RS03605 935 RAFAKSQLGAGTNLPTEGGAFISVRDGDKPAMVEIARRLLEMGFKVMATDGTAFYLKDRGVTgVTIVNKVLE 1006 ***********************************************************99736788999** PP TIGR01369 994 eaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeallea 1051 ++++++++++++++lv+n+t+ +++a++++++irr+a+++++p+ t++++a+a++ea FitnessBrowser__Magneto:AMB_RS03605 1007 GRPHCVDAMMNGQVQLVVNTTE-GSQAVKDSFSIRRTALTNNIPHYTTVAGARAAVEA 1063 *******************997.8889999***********************99987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1052 nodes) Target sequences: 1 (1085 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 31.32 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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