Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate AO356_07480 AO356_07480 carbamoyl phosphate synthase large subunit
Query= BRENDA::P00968
(1073 letters)
>FitnessBrowser__pseudo5_N2C3_1:AO356_07480
Length = 1073
Score = 1603 bits (4151), Expect = 0.0
Identities = 809/1073 (75%), Positives = 919/1073 (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+GVLE+FGV MIGA A
Sbjct: 61 ADATYIEPIKWQTVAKIIEKERPDALLPTMGGQTALNCALDLEREGVLEKFGVEMIGANA 120
Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
D IDKAEDR RFD AMK IGL+ RSGIAH+MEEA AV +GFPCIIRPSFTMGG+GGG
Sbjct: 121 DTIDKAEDRSRFDKAMKSIGLDCPRSGIAHSMEEANAVLERLGFPCIIRPSFTMGGTGGG 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 FEKFA A+ RLTTQMKSVGEVMAIGRT QESLQKALRGLEVG G DPK+ L+DPE+
Sbjct: 361 RFAFEKFAKADARLTTQMKSVGEVMAIGRTFQESLQKALRGLEVGVCGLDPKLDLNDPES 420
Query: 421 LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
++ ++REL GA+RIWY+ADAFRAGL+V+ +F + ID WFLVQIE+L++ EEKV +G
Sbjct: 421 MSVLKRELTVPGAERIWYVADAFRAGLTVEQIFGMNMIDPWFLVQIEDLIKEEEKVKTLG 480
Query: 481 ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540
++ ++ D + +LKRKGF+D RLAKL GV E +R R + ++ PVYKRVDTCAAEFATDT
Sbjct: 481 MSSIDRDTMFRLKRKGFSDMRLAKLLGVTEKSLRAHRHKLEVFPVYKRVDTCAAEFATDT 540
Query: 541 AYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN 600
AY+YSTYEEECEA PST R+KIM+LGGGPNRIGQGIEFDYCCVHA+LALR+DGYETIMVN
Sbjct: 541 AYLYSTYEEECEAAPST-RDKIMILGGGPNRIGQGIEFDYCCVHAALALRDDGYETIMVN 599
Query: 601 CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 660
CNPETVSTDYDTSDRLYFEPVTLEDVLEIVR+EKPKGVIVQYGGQTPLKLARALEAAGVP
Sbjct: 600 CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRVEKPKGVIVQYGGQTPLKLARALEAAGVP 659
Query: 661 VIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVL 720
+IGTSPDAIDRAEDRERFQ VERL L+QP NATV + + A+ A +IGYPLVVRPSYVL
Sbjct: 660 IIGTSPDAIDRAEDRERFQQMVERLNLRQPPNATVRSEDEAIRAAAKIGYPLVVRPSYVL 719
Query: 721 GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME 780
GGRAMEIVY E +L+RY + AV VSND+PVLLDHFL+ A+E+DVDA+ DG+ V+IG IM+
Sbjct: 720 GGRAMEIVYQEDELKRYLREAVQVSNDSPVLLDHFLNCAIEMDVDAVSDGKDVVIGAIMQ 779
Query: 781 HIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI 840
HIEQAGVHSGDSACSLP Y+L IQD MR+QV+K+A EL V GLMNVQ A++ ++Y+I
Sbjct: 780 HIEQAGVHSGDSACSLPPYSLPAHIQDEMREQVKKMALELGVIGLMNVQLALQGEDIYVI 839
Query: 841 EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKF 900
EVNPRA+RTVPFVSK GV LA +AARVMAGK+L E TKE+IP +YSVKE V PF KF
Sbjct: 840 EVNPRASRTVPFVSKCIGVSLAMIAARVMAGKTLKELNFTKEIIPNFYSVKEAVFPFAKF 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 ARDLINLGFEVVATAGTARLIEAAGLKVRRVNKVTEGRPHVVDMIKNDEVTLIINTTEGR 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: 3129
Number of extensions: 135
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 AO356_07480 AO356_07480 (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.29461.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 1572.9 0.0 0 1572.7 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07480 AO356_07480 carbamoyl phosphate
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07480 AO356_07480 carbamoyl phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1572.7 0.0 0 0 1 1052 [] 2 1053 .. 2 1053 .. 0.98
Alignments for each domain:
== domain 1 score: 1572.7 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeelad 61
pkr+dik++l++G+GpivigqA+EFDYsG+qa+kal+eeg++v+Lvnsn+At+mtd+++ad
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07480 2 PKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPAMAD 62
689********************************************************** PP
TIGR01369 62 kvYiePltveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveai 122
++YieP+++++v+kiiekErpDa+l+t+GGqtaLn+a++le++GvLek+gv+++G++ ++i
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07480 63 ATYIEPIKWQTVAKIIEKERPDALLPTMGGQTALNCALDLEREGVLEKFGVEMIGANADTI 123
************************************************************* PP
TIGR01369 123 kkaedRekFkealkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaen 183
+kaedR +F++a+k i+++ ++s i++s+eea ++ e++g+P+i+R++ft+gGtG+gia+n
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07480 124 DKAEDRSRFDKAMKSIGLDCPRSGIAHSMEEANAVLERLGFPCIIRPSFTMGGTGGGIAYN 184
************************************************************* PP
TIGR01369 184 eeelkelvekalkaspikqvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtG 244
+ee++e+++++l++sp+k++l+++sl gwkE+E+EvvRD+kdnciivc+iEn+Dp+GvHtG
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07480 185 REEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKKDNCIIVCSIENFDPMGVHTG 245
************************************************************* PP
TIGR01369 245 dsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvqfaldPeskryvviEvnpRvsR 304
dsi+vaP+qtLtdkeyq+lR+asl+++re+gve++ +nvqf++ P++ r+vviE+npRvsR
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07480 246 DSITVAPAQTLTDKEYQILRNASLAVLREIGVETGgSNVQFGICPNTGRMVVIEMNPRVSR 306
*********************************988************************* PP
TIGR01369 305 ssALAskAtGyPiAkvaaklavGysLdelkndvtk.etvAsfEPslDYvvvkiPrwdldkf 364
ssALAskAtG+PiAkvaaklavGy+Ldel+nd+t+ +t+AsfEPs+DYvv+k+Pr++++kf
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07480 307 SSALASKATGFPIAKVAAKLAVGYTLDELSNDITGgKTPASFEPSIDYVVTKLPRFAFEKF 367
**********************************879************************ PP
TIGR01369 365 ekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllglklk..ekeaesdeeleeal 423
+k+d +l+tqmksvGEvmaigrtf+e+lqkalr le ++ gl+ k + es + l+++l
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07480 368 AKADARLTTQMKSVGEVMAIGRTFQESLQKALRGLEVGVCGLDPKldLNDPESMSVLKREL 428
*****************************************66551045566777889*** PP
TIGR01369 424 kkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkell 484
+ p ++R++++a+a+r+g++ve+++ + id +fl ++++l++ e+++++ ++ ++++++
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07480 429 TVPGAERIWYVADAFRAGLTVEQIFGMNMIDPWFLVQIEDLIKEEEKVKTLGMSSIDRDTM 489
************************************************************* PP
TIGR01369 485 kkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeee 545
++k++Gfsd ++akl++v+e+++r+ r++l++ pv+krvDt+aaEf ++t+YlYstyeee
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07480 490 FRLKRKGFSDMRLAKLLGVTEKSLRAHRHKLEVFPVYKRVDTCAAEFATDTAYLYSTYEEE 550
************************************************************* PP
TIGR01369 546 kddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvstDyd 606
++ +++t++ k+++lG+Gp+Rigqg+EFDyc+vha+lalr+ gy+ti++n+nPEtvstDyd
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07480 551 CEAAPSTRD-KIMILGGGPNRIGQGIEFDYCCVHAALALRDDGYETIMVNCNPETVSTDYD 610
877777777.*************************************************** PP
TIGR01369 607 iadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsaesidra 667
++drLyFe++t+edvl+i++ ek++gvivq+gGqt+l+la++le+agv+i+Gts+++idra
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07480 611 TSDRLYFEPVTLEDVLEIVRVEKPKGVIVQYGGQTPLKLARALEAAGVPIIGTSPDAIDRA 671
************************************************************* PP
TIGR01369 668 EdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneee 728
EdRe+F++++++l++ qp +++++s +ea ++a++igyP++vRpsyvlgGrameiv++e+e
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07480 672 EDRERFQQMVERLNLRQPPNATVRSEDEAIRAAAKIGYPLVVRPSYVLGGRAMEIVYQEDE 732
************************************************************* PP
TIGR01369 729 leryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstl 789
l+ryl+eav+vs+++Pvl+d++l+ a+E+dvDav+dg++v+i +i++HiE+aGvHsGDs++
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07480 733 LKRYLREAVQVSNDSPVLLDHFLNCAIEMDVDAVSDGKDVVIGAIMQHIEQAGVHSGDSAC 793
************************************************************* PP
TIGR01369 790 vlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvsk 850
+lpp +l ++++++++e+vkk+a el v Gl+n+q+++++e++yviEvn+RasRtvPfvsk
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07480 794 SLPPYSLPAHIQDEMREQVKKMALELGVIGLMNVQLALQGEDIYVIEVNPRASRTVPFVSK 854
************************************************************* PP
TIGR01369 851 algvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkst 911
+gv+l+ +a++v++gk+l+el+ +ke +++++vk+avf+f+k+ gvd++lgpemkst
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07480 855 CIGVSLAMIAARVMAGKTLKELNF--TKEIIPNFYSVKEAVFPFAKFPGVDPILGPEMKST 913
*********************775..999******************************** PP
TIGR01369 912 GEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyate 972
GEvmg+g+++ ea++ka++ +++++++ g++++sv+d dk + +a+ l ++g++v+at+
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07480 914 GEVMGVGDTFGEAFAKAQMGASEVLPTGGTAFISVRDDDKPLVAGVARDLINLGFEVVATA 974
************************************************************* PP
TIGR01369 973 gtakvleeagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirreave 1033
gta+ +e ag k++ v+kv+e ++++++++k++e++l+in+t+ ++++ ++y+irr+a++
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07480 975 GTARLIEAAGLKVRRVNKVTEGRPHVVDMIKNDEVTLIINTTE-GRQSIADSYSIRRNALQ 1034
****************************************997.77788899********* PP
TIGR01369 1034 ykvplvteletaealleal 1052
+k+ + t++++ ea++eal
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07480 1035 HKIYCTTTIAAGEAICEAL 1053
**************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: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 11.50
//
[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