Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_090215936.1 CV091_RS06665 carbamoyl-phosphate synthase large subunit
Query= BRENDA::P00968 (1073 letters) >NCBI__GCF_002796795.1:WP_090215936.1 Length = 1120 Score = 1261 bits (3264), Expect = 0.0 Identities = 674/1112 (60%), Positives = 818/1112 (73%), Gaps = 57/1112 (5%) Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60 MPKRTDI+SI+I+GAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDP + Sbjct: 1 MPKRTDIQSIMIIGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPGL 60 Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120 ADATYIEPI EVV KIIEKERPDA+LPTMGGQT LN +L LE GVLE+F V MIGAT Sbjct: 61 ADATYIEPITPEVVAKIIEKERPDALLPTMGGQTGLNTSLALEEMGVLEKFDVEMIGATR 120 Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEE-------------ALAVAADVGFPCI 167 DAI+ AEDR+ F AM ++G+E R+ I ++ AL D+G P I Sbjct: 121 DAIEMAEDRKLFREAMDRLGIENPRASIVTAPKKDNGDADLDEGIRLALQELEDIGLPAI 180 Query: 168 IRPSFTMGGSGGGIAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDN 227 IRP+FTMGG+GGG+AYNRE++ C G+D SP ++L+DESL+GWKEYEMEVVRDK DN Sbjct: 181 IRPAFTMGGTGGGVAYNREDYIHYCRSGMDASPVNQILVDESLLGWKEYEMEVVRDKADN 240 Query: 228 CIIVCSIENFDAMGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFA 287 IIVCSIEN D MG+HTGDSITVAPA TLTDKEYQIMR S+ VLREIGVETGGSNVQ+A Sbjct: 241 AIIVCSIENVDPMGVHTGDSITVAPALTLTDKEYQIMRTHSINVLREIGVETGGSNVQWA 300 Query: 288 VNPKNGRLIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPAS 347 VNP +GR++VIEMNPRVSRSSALASKATGFPIAK+AAKLAVGYTLDEL NDIT TPAS Sbjct: 301 VNPADGRMVVIEMNPRVSRSSALASKATGFPIAKIAAKLAVGYTLDELDNDITKV-TPAS 359 Query: 348 FEPSIDYVVTKIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGAT 407 FEPSIDYVVTKIP+F FEKF G+ LTT MKSVGE M+IGRT ESLQKAL +E G T Sbjct: 360 FEPSIDYVVTKIPKFAFEKFPGSEPYLTTAMKSVGEAMSIGRTIHESLQKALASMESGLT 419 Query: 408 GFD----PKVSL---DDPEALTK--IRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNI 458 GFD P V++ +D A K + + + DR+ IA A R GL+ D + N+T Sbjct: 420 GFDEIAIPGVTVGLWEDAAATDKAAVIKAISQTTPDRMRTIAQAMRHGLTNDEINNVTAF 479 Query: 459 DRWFLVQIEELVRLEEKVAEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRD 518 D WFL +I E+V +E ++ + G+ + D LR +K GF DARL L G E +R+ R Sbjct: 480 DPWFLDRIREIVDMEREIRKNGLP-VREDELRAVKMLGFTDARLGALTGRDEDNVRRARH 538 Query: 519 QYDLHPVYKRVDTCAAEFATDTAYMYSTYEE------ECEANPSTDREKIMVLGGGPNRI 572 + V+KR+DTCAAEF T YMYSTYE ECEA PS DR+K+++LGGGPNRI Sbjct: 539 NLGVKAVFKRIDTCAAEFEAQTPYMYSTYETPMMGEAECEARPS-DRKKVVILGGGPNRI 597 Query: 573 GQGIEFDYCCVHASLALREDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRI 632 GQGIEFDYCC HA AL + GYETIMVNCNPETVSTDYDTSDRLYFEP+TLE V+EI+R+ Sbjct: 598 GQGIEFDYCCCHACYALTDAGYETIMVNCNPETVSTDYDTSDRLYFEPLTLEHVMEILRV 657 Query: 633 EKPKG----VIVQYGGQTPLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLK 688 E+ KG VIVQ+GGQTPLKLA ALE+ G+P++GTSPDAID AEDRERFQ V L LK Sbjct: 658 EQEKGTLHGVIVQFGGQTPLKLANALESEGIPILGTSPDAIDLAEDRERFQALVNELGLK 717 Query: 689 QPANATVTAIEMAVEKAKEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDA 748 QP N + A++ A++IG+PLV+RPSYVLGGRAMEIV D L+RY + AV VS D+ Sbjct: 718 QPKNGIASTDAQAIDIAEKIGFPLVIRPSYVLGGRAMEIVRDMDQLKRYIKEAVVVSGDS 777 Query: 749 PVLLDHFLDDAVEVDVDAICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDV 808 PVLLD +L AVE+DVDAICDG+ V + GIM+HIE+AGVHSGDSACSLP Y+LS+++ D Sbjct: 778 PVLLDSYLAGAVELDVDAICDGKDVHVAGIMQHIEEAGVHSGDSACSLPPYSLSKDVIDR 837 Query: 809 MRQQVQKLAFELQVRGLMNVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARV 868 ++ Q LA L V GLMNVQFA+K++E+YLIEVNPRA+RTVPFV+KAT +A ++ARV Sbjct: 838 IKDQAHSLATALNVVGLMNVQFAIKDDEIYLIEVNPRASRTVPFVAKATDSAIASISARV 897 Query: 869 MAGKSLAEQGVTKEVIP---------------------PYYSVKEVVLPFNKFPGVDPLL 907 MAG+ L+ + P P++SVKE VLPF +FPGVD +L Sbjct: 898 MAGEPLSNFPMRAPYGPDAGYDVNTPIADPMTLADPDMPWFSVKEAVLPFARFPGVDTIL 957 Query: 908 GPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDK-ERVVDLAAKLLK 966 GPEMRSTGEVMG R+FA AF KAQ+G+ + + G A +S+++ DK +++ + A L+ Sbjct: 958 GPEMRSTGEVMGWDRSFAGAFLKAQMGAGMVLPRKGCAFVSIKDSDKSDQMREAAQTLVD 1017 Query: 967 QGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGRRAIEDS 1026 GF L AT GT L GI L NKV+EGRPH+ D +K+G+ ++NTT G +A+EDS Sbjct: 1018 LGFTLVATQGTQAWLDGQGIPCGLTNKVYEGRPHVVDLLKDGKVQILMNTTEGTQAVEDS 1077 Query: 1027 RVIRRSALQYKVHYDTTLNGGFATAMALNADA 1058 + +R AL ++ Y TT G A A+A+ A + Sbjct: 1078 KEMRSVALYGRIPYFTTAAGAHAAALAIKAQS 1109 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: 3137 Number of extensions: 157 Number of successful extensions: 22 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: 1120 Length adjustment: 46 Effective length of query: 1027 Effective length of database: 1074 Effective search space: 1102998 Effective search space used: 1102998 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 WP_090215936.1 CV091_RS06665 (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.3108060.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 1438.2 0.0 0 1438.0 0.0 1.0 1 NCBI__GCF_002796795.1:WP_090215936.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002796795.1:WP_090215936.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1438.0 0.0 0 0 1 1050 [. 2 1103 .. 2 1105 .. 0.95 Alignments for each domain: == domain 1 score: 1438.0 bits; conditional E-value: 0 TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltve 71 pkr+di+++++iG+GpivigqA+EFDYsG+qa+kal+eeg++v+Lvnsn+At+mtd+ lad++YieP+t+e NCBI__GCF_002796795.1:WP_090215936.1 2 PKRTDIQSIMIIGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPGLADATYIEPITPE 72 689******************************************************************** PP TIGR01369 72 avekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineev 142 +v+kiiekErpDa+l+t+GGqt+Ln ++ lee+GvLek++v+++G++ +ai+ aedR++F+ea++ +++e NCBI__GCF_002796795.1:WP_090215936.1 73 VVAKIIEKERPDALLPTMGGQTGLNTSLALEEMGVLEKFDVEMIGATRDAIEMAEDRKLFREAMDRLGIEN 143 *********************************************************************** PP TIGR01369 143 akseivesvee.............aleaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspi 200 ++++iv+ ++ al+ e+ig+P i+R+aft+gGtG+g+a+n+e+ + ++++++asp+ NCBI__GCF_002796795.1:WP_090215936.1 144 PRASIVTAPKKdngdadldegirlALQELEDIGLPAIIRPAFTMGGTGGGVAYNREDYIHYCRSGMDASPV 214 **9999754321122222223333677789***************************************** PP TIGR01369 201 kqvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkii 271 +q+lv++sl gwkE+E+EvvRD++dn+iivc+iEn+Dp+GvHtGdsi+vaP+ tLtdkeyq++R+ s++++ NCBI__GCF_002796795.1:WP_090215936.1 215 NQILVDESLLGWKEYEMEVVRDKADNAIIVCSIENVDPMGVHTGDSITVAPALTLTDKEYQIMRTHSINVL 285 *********************************************************************** PP TIGR01369 272 relgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtket 341 re+gve++ +nvq+a++P + r+vviE+npRvsRssALAskAtG+PiAk+aaklavGy+Ldel nd+tk t NCBI__GCF_002796795.1:WP_090215936.1 286 REIGVETGgSNVQWAVNPADGRMVVIEMNPRVSRSSALASKATGFPIAKIAAKLAVGYTLDELDNDITKVT 356 ******988************************************************************** PP TIGR01369 342 vAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllglkl.... 408 +AsfEPs+DYvv+kiP+++++kf + + l+t mksvGE m+igrt++e+lqkal+s+e++l+g+++ NCBI__GCF_002796795.1:WP_090215936.1 357 PASFEPSIDYVVTKIPKFAFEKFPGSEPYLTTAMKSVGEAMSIGRTIHESLQKALASMESGLTGFDEiaip 427 **************************************************************995532222 PP TIGR01369 409 .......kekeaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvelekele 472 ++++a+++ ++ +a+ +++++R+ +ia+a+r+g++ +e++++t +d +fl++++++v++e+e++ NCBI__GCF_002796795.1:WP_090215936.1 428 gvtvglwEDAAATDKAAVIKAISQTTPDRMRTIAQAMRHGLTNDEINNVTAFDPWFLDRIREIVDMEREIR 498 2222223567788889999***************************************************9 PP TIGR01369 473 eeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstye 543 ++ l +++++l+ +k lGf+d+++++l++ +e++vr++r++lg+ v+kr+Dt+aaEfea+tpY+Ystye NCBI__GCF_002796795.1:WP_090215936.1 499 KNGLP-VREDELRAVKMLGFTDARLGALTGRDEDNVRRARHNLGVKAVFKRIDTCAAEFEAQTPYMYSTYE 568 77776.9***************************************************************9 PP TIGR01369 544 ee.....kddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvstDydiad 609 + + +++ +++kkv++lG+Gp+Rigqg+EFDyc+ ha+ al +agy+ti++n+nPEtvstDyd++d NCBI__GCF_002796795.1:WP_090215936.1 569 TPmmgeaECEARPSDRKKVVILGGGPNRIGQGIEFDYCCCHACYALTDAGYETIMVNCNPETVSTDYDTSD 639 76444334566677889****************************************************** PP TIGR01369 610 rLyFeeltvedvldiiekek....vegvivqlgGqtalnlakeleeagvkilGtsaesidraEdRekFskl 676 rLyFe+lt+e+v++i++ e+ +gvivq+gGqt+l+la++le++g++ilGts+++id aEdRe+F++l NCBI__GCF_002796795.1:WP_090215936.1 640 RLYFEPLTLEHVMEILRVEQekgtLHGVIVQFGGQTPLKLANALESEGIPILGTSPDAIDLAEDRERFQAL 710 ***************998872233568******************************************** PP TIGR01369 677 ldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeavevskekPvli 747 ++elg+kqpk+ +a++ +a +ia++ig+P+++RpsyvlgGrameiv+++++l+ry++eav vs ++Pvl+ NCBI__GCF_002796795.1:WP_090215936.1 711 VNELGLKQPKNGIASTDAQAIDIAEKIGFPLVIRPSYVLGGRAMEIVRDMDQLKRYIKEAVVVSGDSPVLL 781 *********************************************************************** PP TIGR01369 748 dkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvk 818 d yl avE+dvDa++dg++v +agi++HiEeaGvHsGDs+++lpp +ls++v ++ik++++++a++l+v+ NCBI__GCF_002796795.1:WP_090215936.1 782 DSYLAGAVELDVDAICDGKDVHVAGIMQHIEEAGVHSGDSACSLPPYSLSKDVIDRIKDQAHSLATALNVV 852 *********************************************************************** PP TIGR01369 819 GllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkkleele................ 873 Gl+n+qf++kd+e+y+iEvn+RasRtvPfv+ka++ +++++++v++g+ l++ NCBI__GCF_002796795.1:WP_090215936.1 853 GLMNVQFAIKDDEIYLIEVNPRASRTVPFVAKATDSAIASISARVMAGEPLSNFPmrapygpdagydvntp 923 *****************************************************9999************99 PP TIGR01369 874 ...kgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgs 941 ++++ ++vk+av++f+++ gvd +lgpem+stGEvmg +r+++ a+lka++ +++++++kg NCBI__GCF_002796795.1:WP_090215936.1 924 iadPMTLADPDMPWFSVKEAVLPFARFPGVDTILGPEMRSTGEVMGWDRSFAGAFLKAQMGAGMVLPRKGC 994 9985567889999********************************************************** PP TIGR01369 942 vllsvkdkdk.eellelakklaekglkvyategtakvleeagikaevvlkvseeaekilellkeeeielvi 1011 +++s+kd+dk +++ e+a++l+++g++++at+gt++ l +gi + + +kv e ++++++llk++++++++ NCBI__GCF_002796795.1:WP_090215936.1 995 AFVSIKDSDKsDQMREAAQTLVDLGFTLVATQGTQAWLDGQGIPCGLTNKVYEGRPHVVDLLKDGKVQILM 1065 *******999678999******************************************************* PP TIGR01369 1012 nltskkkkaaekgykirreaveykvplvteletaealle 1050 n+t+ +++a+e+++ +r a+ ++p++t++++a+a++ NCBI__GCF_002796795.1:WP_090215936.1 1066 NTTE-GTQAVEDSKEMRSVALYGRIPYFTTAAGAHAAAL 1103 *997.78899999******************99988765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1052 nodes) Target sequences: 1 (1120 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: 0.03u 0.03s 00:00:00.06 Elapsed: 00:00:00.06 # Mc/sec: 18.28 // [ok]
This GapMind analysis is from Jul 26 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